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김경종
2026-05-28 10:57:16 +09:00
parent 1b07531a45
commit 72dad72703
205 changed files with 41703 additions and 80 deletions
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.claude-plugin/marketplace.json
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{
"$schema": "https://anthropic.com/claude-code/marketplace.schema.json",
"name": "agricidaniel-claude-obsidian",
"owner": {
"name": "AgriciDaniel",
"url": "https://github.com/AgriciDaniel"
},
"metadata": {
"description": "claude-obsidian: a self-organizing AI second brain for Obsidian + Claude Code by AgriciDaniel. A persistent, compounding wiki vault of plain Markdown you own, based on Karpathy's LLM Wiki pattern.",
"version": "1.9.2"
},
"plugins": [
{
"name": "claude-obsidian",
"source": "./",
"description": "Claude + Obsidian knowledge companion. v1.7 \"Compound Vault\" + v1.8 methodology modes close 5 of 5 priority gaps from the May 2026 compass artifact. Ships: substrate alignment with kepano/obsidian-skills, default Obsidian CLI transport, hybrid retrieval (Anthropic Sept 2024 contextual retrieval pattern: BM25 + cosine rerank), per-file advisory locking for multi-writer safety, pre-commit verifier agent, AND methodology modes (LYT / PARA / Zettelkasten / Generic) — first-class organizational support no other Claude+Obsidian competitor offers. v1.7.x audit fully closed; 50-query retrieval benchmark verified at +32pp top-1 / +41% error-reduction vs v1.6 baseline. Optional DragonScale Memory extension. Pairs with kepano/obsidian-skills (recommended) for canonical Obsidian primitives.",
"version": "1.9.2",
"author": {
"name": "AgriciDaniel",
"url": "https://github.com/AgriciDaniel"
},
"homepage": "https://github.com/AgriciDaniel/claude-obsidian",
"repository": "https://github.com/AgriciDaniel/claude-obsidian",
"license": "MIT"
}
]
}
.claude-plugin/plugin.json
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{
"name": "claude-obsidian",
"version": "1.9.2",
"description": "Claude + Obsidian knowledge companion. Sets up a persistent, compounding wiki vault (Karpathy's LLM Wiki pattern). v1.7 \"Compound Vault\" + v1.8 methodology modes close 5 of 5 priority gaps from the May 2026 compass artifact. Ships: substrate alignment with kepano/obsidian-skills, default Obsidian CLI transport, hybrid retrieval (contextual prefix + BM25 + cosine rerank per Anthropic's Sept 2024 research), per-file advisory locking for multi-writer safety, pre-commit verifier agent, AND methodology modes (LYT / PARA / Zettelkasten / Generic) for first-class organizational support no other Claude+Obsidian competitor offers. v1.7.x audit closure: every BLOCKER + HIGH + MEDIUM + LOW finding from the v1.7.0 audit is CLOSED or DEFERRED-with-rationale. Optional DragonScale Memory extension (log folds, deterministic addresses, semantic tiling lint, boundary-first autoresearch).",
"author": {
"name": "AgriciDaniel",
"url": "https://github.com/AgriciDaniel"
},
"license": "MIT",
"homepage": "https://github.com/AgriciDaniel/claude-obsidian",
"repository": "https://github.com/AgriciDaniel/claude-obsidian",
"keywords": [
"obsidian",
"knowledge-base",
"wiki",
"memory",
"notetaker",
"second-brain",
"vault",
"markdown",
"cross-project",
"llm-wiki",
"karpathy",
"pkm",
"canvas",
"visual"
]
}
.cursor/rules/claude-obsidian.mdc
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---
description: claude-obsidian: LLM Wiki Pattern for Obsidian vaults. Always-on context for any project pointed at this repo.
globs:
- "wiki/**/*.md"
- ".raw/**/*"
- "skills/**/SKILL.md"
alwaysApply: true
---
# claude-obsidian
A Claude Code plugin and Obsidian vault that builds persistent, compounding knowledge bases using Andrej Karpathy's LLM Wiki pattern. This repo works with Cursor's AI through the cross-platform Agent Skills format.
## What This Project Is
- **Vault root**: contains `wiki/` (agent-generated knowledge) and `.raw/` (source documents: immutable)
- **Hot cache**: `wiki/hot.md` (~500 tokens) holds recent session context
- **Index**: `wiki/index.md` is the master catalog Claude reads first
- **Skills**: 10 skills under `skills/<name>/SKILL.md` define ingest/query/lint/save/canvas/etc
## Skills Available
| Skill | When to use |
|---|---|
| `wiki` | Scaffold new vault, route to sub-skills |
| `wiki-ingest` | Ingest a file, URL, or image: creates 8-15 wiki pages |
| `wiki-query` | Answer questions from the wiki (Quick / Standard / Deep modes) |
| `wiki-lint` | Health check: orphans, dead links, gaps |
| `save` | File current conversation as a wiki note |
| `autoresearch` | Autonomous research loop |
| `canvas` | Create/edit Obsidian canvas files |
| `defuddle` | Clean web pages before ingest |
| `obsidian-markdown` | Obsidian syntax reference |
| `obsidian-bases` | Obsidian Bases (.base files) |
Read the relevant `skills/<name>/SKILL.md` file when the user's request matches a skill's trigger phrases.
## Critical Conventions
1. **Never modify `.raw/`**. Sources are immutable
2. **Read `wiki/hot.md` first** when starting a session (if it exists)
3. **Use wikilinks** (`[[Note Name]]`) for all internal references in wiki pages
4. **Frontmatter is flat YAML**. See `skills/wiki/references/frontmatter.md`
5. **Append to `wiki/log.md`**, never edit past entries
6. **Hot cache is overwritten** at session end (it's a cache, not a journal)
## Setup for Cursor
To make these skills first-class in Cursor, run:
```bash
ln -s "$(pwd)/skills" .cursor/skills
```
Or use the bundled installer:
```bash
bash bin/setup-multi-agent.sh
```
## Cross-Reference
- Plugin: https://github.com/AgriciDaniel/claude-obsidian
- Pattern: https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f
- Related: https://github.com/kepano/obsidian-skills
.github/FUNDING.yml
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custom:
- https://www.skool.com/ai-marketing-hub-pro
.github/ISSUE_TEMPLATE/bug_report.md
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---
name: Bug report
about: Something is broken or behaves unexpectedly
title: "[bug] "
labels: bug
assignees: ''
---
## What happened
A clear description of the unexpected behavior.
## Expected behavior
What you expected to happen instead.
## Reproduction steps
1. ...
2. ...
3. ...
## Environment
- Plugin version: (e.g. v1.9.0)
- Claude Code version: (run `claude --version`)
- OS: (e.g. macOS 14.5, Pop!_OS 24.04, Windows 11)
- Obsidian version: (if relevant)
- Transport selected: (filesystem / obsidian-cli / mcp-obsidian — see `.vault-meta/transport.json`)
## Skill / agent / script involved
Which surface is affected? (e.g. `/wiki-ingest`, `scripts/wiki-mode.py`, `agents/verifier.md`)
## Logs / output
```
Paste relevant terminal output or error messages here.
```
## What you tried
- [ ] Ran `make test` — all 8 suites green? Yes / No
- [ ] Checked CHANGELOG for known issues at your version
- [ ] Searched existing issues for similar reports
## Additional context
Anything else that might help (screenshots, related issues, recent changes).
.github/ISSUE_TEMPLATE/feature_request.md
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---
name: Feature request
about: Suggest an idea, new skill, or enhancement
title: "[feature] "
labels: enhancement
assignees: ''
---
## Problem
What user need or workflow gap motivates this request? Be specific about the situation where today's behavior falls short.
## Proposed solution
Describe what you'd like to see. New skill? New agent? Change to an existing one? Sketch the interface (slash command, trigger phrases, expected output).
## Alternatives considered
What other approaches did you think about, and why is this one preferred?
## Scope
Which existing surface(s) does this touch?
- [ ] A new skill (`skills/<name>/`)
- [ ] A new agent (`agents/<name>.md`)
- [ ] A new script (`scripts/<name>`)
- [ ] Change to existing skill: (which?)
- [ ] Change to plugin manifest / hooks / setup scripts
- [ ] Documentation only
## Compatibility
- Does this change behavior for existing v1.x vaults? Yes / No
- Does it require a new opt-in (`bin/setup-*.sh`)? Yes / No
- Does it introduce a new dependency? Yes / No
## Testing
How would this be tested hermetically? (No network, no external services.)
## Additional context
Links, examples, or references to similar features in other tools.
.github/copilot-instructions.md
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# claude-obsidian: GitHub Copilot Instructions
This repository is a **Claude Code plugin and Obsidian vault** that builds persistent, compounding knowledge bases using Andrej Karpathy's LLM Wiki pattern. It is markdown-only. No build step, no compiled code, no runtime dependencies.
## Project Type
- Agent Skills package (cross-platform Agent Skills standard)
- Obsidian vault (interpretable by Obsidian directly)
- Claude Code plugin (installable via marketplace)
## Repository Layout
- `skills/`: 10 skills, each with a `SKILL.md` defining trigger phrases and instructions
- `hooks/hooks.json`: Claude Code lifecycle hooks (SessionStart, PostCompact, PostToolUse, Stop)
- `.claude-plugin/plugin.json`: plugin manifest
- `wiki/`: generated knowledge base (Markdown files with YAML frontmatter)
- `.raw/`: immutable source documents (never modify)
- `_templates/`: Obsidian Templater templates
- `_attachments/`: images and PDFs referenced by wiki pages
## Conventions Copilot Should Follow
When suggesting edits:
1. **Frontmatter is flat YAML** with plural keys: `tags`, `aliases`, `cssclasses`
2. **Internal links are wikilinks**: `[[Note Name]]`, not Markdown links to `.md` paths
3. **Dates are `YYYY-MM-DD`**, not ISO datetimes
4. **`.raw/` is immutable**. Never suggest edits to anything under that path
5. **`wiki/log.md` is append-only**, with new entries at the top
6. **`wiki/hot.md` is overwritten** at session end, not appended to
7. **Skills use only `name` and `description` in frontmatter**. No `allowed-tools`, no `triggers`, no `globs` (these are not part of the Agent Skills spec)
8. **Custom callouts**: this vault defines `[!contradiction]`, `[!gap]`, `[!key-insight]`, `[!stale]` in `.obsidian/snippets/vault-colors.css`. These render only with that snippet enabled.
## When Editing Skills (`skills/<name>/SKILL.md`)
- Frontmatter: `name` (matches directory name) and `description` (single quoted line, max ~250 useful chars)
- Body: short, imperative instructions. Reference files with backticks. Do not paste large code blocks unless they're essential.
- Trigger phrases go in the `description` field, not in body or non-standard fields
## When Editing Hooks (`hooks/hooks.json`)
- Valid event names only: `SessionStart`, `Stop`, `PreToolUse`, `PostToolUse`, `PreCompact`, `PostCompact`, `UserPromptSubmit`
- Hook types: `command` (shell), `prompt` (LLM), `http` (POST), `agent` (subagent)
- `matcher` field uses regex against tool names for `PreToolUse`/`PostToolUse`
- For `SessionStart`: matcher uses `startup`, `resume`, `clear`, or `compact`
## Cross-Reference
- Plugin: https://github.com/AgriciDaniel/claude-obsidian
- Pattern source: https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f
- Authoritative Obsidian-specific skills: https://github.com/kepano/obsidian-skills
.github/pull_request_template.md
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# Pull request
## Summary
One-paragraph description of what this PR changes and why.
## Type
- [ ] Bug fix (`fix:`)
- [ ] New feature (`feat:`)
- [ ] Documentation (`docs:`)
- [ ] Refactor (`refactor:`)
- [ ] Test coverage (`test:`)
- [ ] Chore / build / maintenance (`chore:`)
## Related issue
Closes #<issue-number> (if applicable)
## Changes
List the files and surfaces touched:
- `skills/<name>/SKILL.md` — what changed
- `scripts/<name>.py` — what changed
- ...
## Six-cut self-review
- [ ] Read every file before changing it
- [ ] New identifiers named for the next reader
- [ ] Smallest unit that works (no speculative abstraction)
- [ ] Deletions kept up with additions where applicable
- [ ] New behavior has hermetic test coverage
- [ ] New failure modes have explicit handling + undo plan
## Testing
```
make test
```
Paste the tail of the output here (or a summary if too long):
```
All tests passed.
```
## Verifier
For non-trivial changes, dispatch `agents/verifier.md` on the staged diff and paste its verdict:
- Verdict: SHIP / HOLD-FIX-FIRST / NEEDS-REWORK
- BLOCKER: N / HIGH: N / MEDIUM: N / LOW: N
## CHANGELOG
- [ ] Added an entry under `## [Unreleased]` in `CHANGELOG.md`
## Screenshots / output
If the change affects user-visible output, paste a before/after example.
## Notes for reviewer
Anything specific the reviewer should focus on, or context that's not obvious from the diff.
.github/workflows/test.yml
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name: Tests
on:
push:
branches: [main]
pull_request:
branches: [main]
workflow_dispatch:
jobs:
test:
name: Hermetic test suite
runs-on: ubuntu-latest
timeout-minutes: 5
steps:
- name: Checkout
uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.11'
- name: Verify Python version
run: python3 --version
- name: Verify Bash + GNU coreutils
run: bash --version && date --version | head -1
- name: Make scripts executable
run: chmod +x scripts/*.sh scripts/*.py bin/*.sh tests/*.sh 2>/dev/null || true
- name: Run hermetic test suite
run: make test
- name: Verify wiki-mode CLI surfaces
run: |
python3 scripts/wiki-mode.py get
python3 scripts/wiki-mode.py config | python3 -m json.tool > /dev/null
python3 scripts/wiki-mode.py id
python3 scripts/wiki-mode.py templates
- name: Verify transport detection
run: bash scripts/detect-transport.sh --peek | python3 -m json.tool > /dev/null
lint-skills:
name: Skill frontmatter validation
runs-on: ubuntu-latest
timeout-minutes: 2
steps:
- name: Checkout
uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.11'
- name: Install PyYAML
run: pip install pyyaml
- name: Validate every SKILL.md has valid YAML frontmatter
run: |
python3 <<'PYEOF'
import os, sys, yaml
errors = []
for root, dirs, files in os.walk('skills'):
for f in files:
if f == 'SKILL.md':
path = os.path.join(root, f)
with open(path) as fh:
content = fh.read()
if not content.startswith('---'):
errors.append(f"{path}: missing frontmatter")
continue
try:
end = content.index('\n---', 4)
frontmatter = yaml.safe_load(content[4:end])
if not frontmatter.get('name'):
errors.append(f"{path}: missing 'name' in frontmatter")
if not frontmatter.get('description'):
errors.append(f"{path}: missing 'description' in frontmatter")
except Exception as e:
errors.append(f"{path}: frontmatter parse error: {e}")
if errors:
print("\n".join(errors))
sys.exit(1)
print("All SKILL.md files have valid frontmatter.")
PYEOF
- name: Validate every agent has tools declared
run: |
python3 <<'PYEOF'
import os, sys, yaml
errors = []
for f in os.listdir('agents'):
if f.endswith('.md'):
path = os.path.join('agents', f)
with open(path) as fh:
content = fh.read()
if not content.startswith('---'):
errors.append(f"{path}: missing frontmatter")
continue
try:
end = content.index('\n---', 4)
frontmatter = yaml.safe_load(content[4:end])
if not frontmatter.get('tools'):
errors.append(f"{path}: missing 'tools' in frontmatter")
except Exception as e:
errors.append(f"{path}: frontmatter parse error: {e}")
if errors:
print("\n".join(errors))
sys.exit(1)
print("All agents have tools declared.")
PYEOF
- name: Validate plugin.json + marketplace.json
run: |
python3 -c "import json; json.load(open('.claude-plugin/plugin.json'))"
python3 -c "import json; json.load(open('.claude-plugin/marketplace.json'))"
python3 -c "import json; json.load(open('hooks/hooks.json'))"
echo "All plugin manifests are valid JSON."
.gitignore
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# Obsidian
# workspace.json is intentionally tracked — ships with pre-configured graph view
# .obsidian/workspace.json
.obsidian/workspace-mobile.json
.obsidian/workspace-visual.json
.obsidian/plugins/*/data.json
!.obsidian/plugins/calendar/data.json
!.obsidian/plugins/thino/data.json
# Excalidraw main.js is 8MB — downloaded by setup-vault.sh, not tracked in git
.obsidian/plugins/obsidian-excalidraw-plugin/main.js
# Large binary assets — add your own images to _attachments/images/
# Uncomment the line below to exclude images from git (recommended for large vaults)
# _attachments/images/
.smart-connections/
.obsidian-git-data
.trash/
# System
.DS_Store
Thumbs.db
# Python
__pycache__/
*.pyc
.venv/
# Node
node_modules/
# Local secrets
.env
.env.local
*.local.md
# Private keys and credentials (defense-in-depth, catches accidental drops)
*.pem
*.key
*.p12
*.pfx
*.jks
id_rsa*
id_ed25519*
id_ecdsa*
id_dsa*
credentials*
secrets.y*ml
auth.json
# Personal files dropped into vault root by Obsidian (don't commit these)
WIKI*.md
PROMPT.md
Welcome.md
*.tmp.*
Obsidian vault*
Untitled.canvas
Cosmic Brain*.gif
Cosmic Brain*.png
Untitled *.canvas
Untitled.base
*.base
# Track our committed dashboard.base (Bases dashboard shipped with the vault)
!wiki/meta/dashboard.base
# Scratch canvases and personal vault files
Banana Images.canvas
Demo Images.canvas
*Images.canvas
# Daily notes created by Calendar plugin
????-??-??.md
# Video and large media files
*.mkv
*.mp4
*.mov
*.avi
# Transcripts (copyright — do not commit)
*Trascipt*.txt
*Transcript*.txt
# Personal images dropped in vault root
cosmic code.png
_attachments/code-genesis.png
_attachments/neural-voyager.png
_attachments/the-frontier.png
# Excalidraw drawings (personal, user-specific)
Excalidraw/
# Loose brand/personal GIFs and images in vault root (not _attachments/)
Claude SEO*.gif
Claude SEO*.png
# Private Skool Hub assets — not for public repos
_attachments/images/skool-hub/
# Archive of old versions (cosmic-brain, GIF assets)
claude-obsidian-archive/
# Sibling-plugin marketing assets that landed in working tree (claude-canvas covers / tutorials)
claude-canvas-covers and stuff/
claude-canvas/
# Codex CLI sentinel marker (0-byte read-only file created by `codex` runs)
.codex
# User-specific attachments
_attachments/
# DragonScale runtime lockfiles and local caches (flock + embedding cache; state files like counter.txt and thresholds.json ARE tracked)
.vault-meta/.address.lock
.vault-meta/.tiling.lock
.vault-meta/tiling-cache.json
.vault-meta/tiling-cache.*.tmp
# v1.7 Compound Vault runtime artifacts (regenerable; host-specific)
.vault-meta/.wiki-lock.meta
.vault-meta/.bm25.lock
.vault-meta/.embed-cache.lock
.vault-meta/locks/*
!.vault-meta/locks/.gitkeep
.vault-meta/chunks/
.vault-meta/bm25/
.vault-meta/embed-cache.json
.vault-meta/embed-cache.*.tmp
.vault-meta/transport.json
.vault-meta/transport.*.tmp
.vault-meta/hook.log
# v1.8 methodology mode (host-specific by default; `git add -f` to commit if desired)
.vault-meta/mode.json
.vault-meta/mode.*.tmp
.obsidian/app.json
Vendored
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{}
{
"userIgnoreFilters": [
"agents/",
"commands/",
"hooks/",
"skills/",
"_templates/",
"README.md",
"CLAUDE.md",
"WIKI.md",
"Welcome.md"
]
}
.obsidian/appearance.json
Vendored
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{}
{
"enabledCssSnippets": [
"vault-colors",
"ITS-Dataview-Cards",
"ITS-Image-Adjustments"
]
}
.obsidian/community-plugins.json
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[
"obsidian-excalidraw-plugin",
"obsidian-banners",
"calendar",
"thino"
]
.obsidian/graph.json
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{
"collapse-filter": true,
"search": "",
"collapse-filter": false,
"search": "path:wiki",
"showTags": false,
"showAttachments": false,
"hideUnresolved": false,
"showOrphans": true,
"collapse-color-groups": true,
"colorGroups": [],
"hideUnresolved": true,
"showOrphans": false,
"collapse-color-groups": false,
"colorGroups": [
{
"query": "path:wiki/entities",
"color": {
"a": 1,
"rgb": 12945088
}
},
{
"query": "path:wiki/concepts",
"color": {
"a": 1,
"rgb": 5227007
}
},
{
"query": "path:wiki/sources",
"color": {
"a": 1,
"rgb": 6986069
}
},
{
"query": "path:wiki/questions",
"color": {
"a": 1,
"rgb": 14474410
}
},
{
"query": "path:wiki/comparisons",
"color": {
"a": 1,
"rgb": 13724009
}
},
{
"query": "path:wiki/meta",
"color": {
"a": 1,
"rgb": 5676246
}
},
{
"query": "path:wiki",
"color": {
"a": 1,
"rgb": 4473924
}
}
],
"collapse-display": true,
"showArrow": false,
"textFadeMultiplier": 0,
"nodeSizeMultiplier": 1,
"lineSizeMultiplier": 1,
"collapse-forces": true,
"centerStrength": 0.518713248970312,
"repelStrength": 10,
"showArrow": true,
"textFadeMultiplier": -1,
"nodeSizeMultiplier": 2,
"lineSizeMultiplier": 0.8,
"collapse-forces": false,
"centerStrength": 0.25,
"repelStrength": 20,
"linkStrength": 1,
"linkDistance": 250,
"scale": 1,
"linkDistance": 80,
"scale": 0.5191098990818888,
"close": true
}
.obsidian/plugins/calendar/data.json
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{
"shouldConfirmBeforeCreate": false,
"localeOverride": "en-GB",
"weekStart": "monday",
"showWeeklyNote": false,
"sourceSettings": {
"wordCount": {
"color": "#ebcb8b",
"display": "calendar-and-menu",
"wordsPerDot": 250
},
"tasks": {
"color": "#d08770",
"display": "calendar-and-menu",
"maxIncompleteTaskDots": 1
},
"links": {
"color": "#a3be8c",
"display": "menu"
},
"backlinks": {
"color": "#5e81ac",
"display": "menu"
},
"zettels": {
"color": "#b48ead",
"display": "calendar-and-menu"
},
"emoji-tags": {
"display": "none"
}
},
"showNoteIndicator": true
}
.obsidian/plugins/calendar/main.js
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.obsidian/plugins/calendar/manifest.json
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{
"id": "calendar-beta",
"name": "Calendar (Beta)",
"description": "Calendar view of your daily notes",
"version": "2.0.0",
"author": "Liam Cain",
"authorUrl": "https://github.com/liamcain/",
"isDesktopOnly": false,
"minAppVersion": "0.9.11"
}
.obsidian/plugins/calendar/styles.css
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button:focus {
box-shadow: 0 0 0 1px var(--interactive-accent);
}
#calendar-container [data-emoji-tag]::after {
content: attr(data-emoji-tag);
position: absolute;
top: -4px;
right: 4px;
height: 8px;
width: 8px;
z-index: 1;
}
.obsidian/plugins/obsidian-banners/main.js
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.obsidian/plugins/obsidian-banners/manifest.json
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{
"id": "obsidian-banners",
"name": "Banners",
"description": "Add banner images to your notes!",
"version": "1.3.3",
"minAppVersion": "0.13.21",
"author": "Danny Hernandez",
"authorUrl": "https://github.com/noatpad",
"isDesktopOnly": false
}
.obsidian/plugins/obsidian-banners/styles.css
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.obsidian/plugins/obsidian-excalidraw-plugin/manifest.json
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{
"id": "obsidian-excalidraw-plugin",
"name": "Excalidraw",
"version": "2.22.0",
"minAppVersion": "1.5.7",
"description": "Sketch Your Mind. An Obsidian plugin to edit and view Excalidraw drawings. Enter the world of 4D Visual PKM.",
"author": "Zsolt Viczian",
"authorUrl": "https://excalidraw-obsidian.online",
"fundingUrl": "https://ko-fi.com/zsolt",
"helpUrl": "https://github.com/zsviczian/obsidian-excalidraw-plugin#readme",
"isDesktopOnly": false
}
.obsidian/plugins/obsidian-excalidraw-plugin/styles.css
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.obsidian/plugins/thino/data.json
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{
"FirstLoaded": true,
"StartDate": "Sunday",
"InsertAfter": "",
"UserName": "THINO 😉",
"ProcessEntriesBelow": "",
"Language": "en",
"SaveMemoButtonLabel": "NOTE",
"SaveMemoButtonIcon": "",
"ShareFooterStart": "{ThinoNum} Thino {UsedDay} Day",
"ShareFooterEnd": "✍️ by {UserName}",
"DefaultPrefix": "List",
"DefaultTimePrefix": "HH:mm",
"UseDailyOrPeriodic": "Daily",
"InsertDateFormat": "Tasks",
"DefaultEditorLocation": "Top",
"UseButtonToShowEditor": false,
"FocusOnEditor": true,
"ShowClipboardOnFocus": true,
"OpenDailyMemosWithMemos": true,
"HideDoneTasks": false,
"ShowTaskLabel": true,
"AppendDateWhenTaskDone": false,
"MobileAndDesktop": "All",
"OpenMemosAutomatically": false,
"ShowScrollbar": false,
"ShowTime": true,
"ShowDate": true,
"AddBlankLineWhenDate": false,
"AutoSaveWhenOnMobile": false,
"DeleteFileName": "delete",
"QueryFileName": "query",
"UseVaultTags": false,
"SetCustomBackgroundImage": false,
"SetCustomMemoFooter": false,
"DefaultLightBackgroundImage": "",
"DefaultDarkBackgroundImage": "",
"DefaultLightBackgroundImageForClean": "",
"DefaultDarkBackgroundImageForClean": "",
"DefaultMemoComposition": "{TIME} {CONTENT}",
"CommentOnMemos": false,
"CommentsInOriginalNotes": false,
"FetchMemosMark": "#memo",
"FetchMemosFromNote": false,
"ShowCommentOnMemos": false,
"ShowLeftSideBar": false,
"MemoListView": "list",
"MemoSaveLocation": "DAILY",
"MemoOtherSaveLocation": {
"MemoDefaultCanvasPath": "basic.thino.canvas",
"MemoDefaultMultiFilePath": "Thino",
"MemoDefaultSingleFilePath": "basic.thino.md"
},
"JournalSettings": {
"granularity": "day",
"useIndependentSettings": false,
"headingDateFormat": "YYYY-MM-DD",
"daily": {
"folder": "",
"format": "YYYY-MM-DD",
"template": ""
},
"weekly": {
"folder": "",
"format": "gggg-[W]ww",
"template": ""
},
"monthly": {
"folder": "",
"format": "YYYY-MM",
"template": ""
},
"yearly": {
"folder": "",
"format": "YYYY",
"template": ""
}
},
"MemoDailyTarget": 5,
"HeatmapColorScheme": "default",
"EnabledHttpApi": false,
"HttpApiIpType": "127.0.0.1",
"HttpApiPort": "43999",
"AutoDownloadImage": false,
"EditorType": "obsidian",
"EnabledLocationList": [
{
"value": "DAILY",
"target": "ProcessEntriesBelow",
"insert": "InsertAfter"
}
],
"DeleteThinoDirectly": false,
"CaptureKey": {
"EnableCaptureKey": false,
"OpenThinoGlobally": "CommandOrControl+Shift+T",
"ShowNearMouse": false
},
"startSync": false,
"tokenForVerify": {},
"saveThinoType": "FILE",
"showDayMark": false,
"dayMarkRange": "day",
"navigation": false,
"password": "",
"needVerify": false,
"addTagAutomatically": false,
"addTagPosition": "End",
"addTagWithNewline": false,
"chatViewStyle": "default",
"MomentsBackgroundImage": "https://images.pexels.com/photos/531767/pexels-photo-531767.jpeg",
"MomentsIcon": "https://images.pexels.com/photos/256514/pexels-photo-256514.jpeg",
"MomentsQuote": "Share your thino with the world",
"DefaultThemeForThino": "modern",
"LastUpdatedVersion": "3.0.4",
"ShareToThinoWithText": false,
"ShareToThinoWithTextAppend": "",
"ShareToThinoWithTextPrepend": "",
"ShareToThinoWithTextNewline": "none",
"hidePinnedGroup": false,
"DifferentInsertTarget": false,
"InsertAfterForTask": "",
"ProcessContentTarget": "custom",
"InsertType": "custom",
"ShareAppendType": "preset",
"SharePrependType": "preset",
"SetFileNameAfterCreate": false,
"TagForFileTypeFiles": "thino/file",
"TagForMultiTypeFiles": "thino/multi",
"MinHeightForShare": "200px",
"ThinoMaxHeight": 0,
"ThinoCollapsedHeight": 100,
"OptimizeForCallout": true,
"AppendOrPrependTextViaServer": false,
"AppendViaServer": "",
"PrependViaServer": "",
"WithNewLineViaServer": "none",
"SupportSelectOtherView": false,
"WaitTemplaterToFinishParse": false,
"NavbarButton": false,
"AlwaysShowStatusText": false,
"FilterByMetadata": false,
"ShowSourcePath": false,
"ShowUpdateMessage": true,
"SyncManually": false,
"MemoFixedPrefix": "",
"MemoFixedSuffix": "",
"UseMemoFixedStrings": false,
"enableWordCount": false,
"maxWordCount": 0,
"enableReferenceLinksGroup": false,
"doubleClickBehavior": "edit-thino",
"useMobileViewDefaultHeader": false,
"IgnoreFolderForMultiType": [],
"UseBlockLinkWhenDragging": false,
"ShowScrollToTopButton": true,
"ZoomImageWhenViewing": false,
"ViewArchiveInRandomReview": false,
"DraggingBehavior": "block-link",
"superEnabled": false,
"enableSecretMasking": false,
"secretContentRegex": "",
"secretMaskingStyle": "blur",
"fsrsRequestRetention": 0.9,
"fsrsMaximumInterval": 36500,
"fsrsEnableFuzz": true,
"fsrsEnableShortTerm": true,
"fsrsWeights": [],
"fsrsDailyLimit": 100,
"wechat": {
"enabled": false,
"autoStart": false,
"defaultReply": "",
"voiceSaveMode": "both",
"agentRouting": {
"enabled": false,
"defaultAgent": "claude",
"agents": {
"claude": {
"type": "cli",
"command": "claude",
"aliases": [
"cc"
]
},
"codex": {
"type": "cli",
"command": "codex",
"aliases": [
"cx"
]
},
"gemini": {
"type": "cli",
"command": "gemini",
"aliases": [
"gm"
]
}
}
}
},
"general": {
"tokenExpiresAt": 0,
"userInfo": null
}
}
.obsidian/plugins/thino/main.js
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.obsidian/plugins/thino/manifest.json
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{
"id": "obsidian-memos",
"name": "Thino",
"description": "Capturing ideas and save them into daily notes. (Closed source)",
"version": "3.0.4",
"author": "Boninall",
"authorUrl": "https://github.com/Quorafind/",
"isDesktopOnly": false,
"minAppVersion": "1.0.0"
}
.obsidian/plugins/thino/styles.css
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.obsidian/snippets/ITS-Dataview-Cards.css
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/* ITS Dataview Cards — by SlRvb
* Source: https://github.com/SlRvb/Obsidian--ITS-Theme
* License: GPL-2.0 (https://github.com/SlRvb/Obsidian--ITS-Theme/blob/main/LICENSE)
*/
.dvl-c .table-view-table > thead::before {
content: "⚙";
font-family: var(--its, var(--default-font));
float: right;
padding: 5px 10px 5px 10px;
}
.dvl-c .table-view-table > thead > tr {
display: flex;
flex-direction: row;
border: 1px solid var(--outline, var(--background-modifier-box-shadow));
margin: 0;
flex-wrap: wrap;
border-radius: var(--radius, 3px);
}
.dvl-c table .table-view-table > thead > tr {
position: absolute;
right: 0;
}
.dvl-c .table-view-table > thead:not(:hover) > * {
display: none;
}
.dvl-c .dataview th {
font-family: var(--default-font);
background: var(--note, var(--background-primary));
font-size: var(--f-s-text, var(--editor-font-size));
border: 0;
color: var(--text, var(--text-normal));
opacity: 1;
}
.dvl-c .dataview th:hover {
background: var(--td, var(--background-modifier-form-field));
}
.dvl-c .list-view-ul li, .dvl-c .dataview.table-view-table > tbody > tr {
display: flex;
flex-direction: column;
background-color: var(--aside-bg, var(--background-primary-alt));
box-shadow: var(--outline, var(--background-modifier-box-shadow)) 0px 0px 0px 1px, var(--outline, var(--background-modifier-box-shadow)) 0px 2px 4px;
margin: 5px 0;
padding: 10px;
border-radius: var(--radius, 3px);
border: 0;
}
.dvl-c .list-view-ul, .dvl-c .dataview.table-view-table > tbody.table-view-tbody {
display: flex;
flex-direction: row;
flex-wrap: wrap;
padding-inline-start: 0;
}
.dvl-c .block-language-dataviewjs .dataview-result-list-li, .dvl-c .list-view-ul li, .dvl-c .dataview.table-view-table > tbody > tr {
flex: 1 0 150px;
margin: 10px;
}
.dvl-c .dataview.dataview.table-view-table td {
padding: 0;
background-color: transparent;
border: 0;
}
.dvl-c .list-view-ul li::before {
display: none;
}
.dvl-c .dataview.table-view-table li {
box-shadow: none;
border: 0;
padding: 0;
}
.obsidian/snippets/ITS-Image-Adjustments.css
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/* ITS Image Adjustments — by SlRvb
* Source: https://github.com/SlRvb/Obsidian--ITS-Theme
* License: GPL-2.0 (https://github.com/SlRvb/Obsidian--ITS-Theme/blob/main/LICENSE)
*/
body {
--image-border-color: var(--background-modifier-border);
--image-border-width: 1px;
--image-border-padding: 8px;
--image-border-background: var(--td);
}
/*----Image Positions/Adjustments----*/
body {
--micro: 70px;
--tiny: 100px;
--small: 200px;
--small-med: 300px;
--med-small: 400px;
--medium: 500px;
--med-tall: 600px;
--tall: 700px;
}
.popover.hover-popover {
--micro: 70px;
--tiny: 100px;
--small: 150px;
--small-med: 200px;
--med-small: 250px;
--medium: 300px;
--med-tall: 450px;
--tall: 500px;
}
/*----Mobile----*/
@media (max-width: 500px) {
.theme-dark, .theme-light {
/*Mobile Sizes*/
--radius: 0px;
--micro: 70px;
--tiny: 100px;
--small: 150px;
--small-med: 200px;
--med-small: 250px;
--medium: 300px;
--med-tall: 450px;
--tall: 500px;
}
}
/*-Image Sizing-*/
/*Fit image within bounds WITHOUT stretching*/
img:is([alt*=cover], [alt*=cvr]),
.image-embed:is([src*="#cover"], [src*="#cvr"]),
span.image-embed:is([src*="#cover"], [src*="#cvr"]) img {
object-fit: cover;
}
:is(.view-content, .popover) img[alt][alt]:not([alt*=relative]):is([alt*=wmicro],
[alt*=wtiny],
[alt*=wsmall],
[alt*=ws-med],
[alt*=wm-sm],
[alt*=wmed],
[alt*=wm-tl],
[alt*=wtall],
[alt*=wfull]) {
width: var(--image-adj-size-w);
}
:is(.view-content, .popover) img[alt][alt]:not([alt*=relative]):is([alt*=hmicro],
[alt*=htiny],
[alt*=hsmall],
[alt*=hs-med],
[alt*=hm-sm],
[alt*=hmed],
[alt*=hm-tl],
[alt*=htall],
[alt*=hfull]) {
height: var(--image-adj-size-h);
}
:is(.view-content, .popover) img[alt][alt]:not([alt*=relative])[alt*=hmicro] {
--image-adj-size-h: var(--micro);
}
:is(.view-content, .popover) img[alt][alt]:not([alt*=relative])[alt*=htiny] {
--image-adj-size-h: var(--tiny);
}
:is(.view-content, .popover) img[alt][alt]:not([alt*=relative])[alt*=hsmall] {
--image-adj-size-h: var(--small);
}
:is(.view-content, .popover) img[alt][alt]:not([alt*=relative])[alt*=hs-med] {
--image-adj-size-h: var(--small-med);
}
:is(.view-content, .popover) img[alt][alt]:not([alt*=relative])[alt*=hm-sm] {
--image-adj-size-h: var(--med-small);
}
:is(.view-content, .popover) img[alt][alt]:not([alt*=relative])[alt*=hmed] {
--image-adj-size-h: var(--medium);
}
:is(.view-content, .popover) img[alt][alt]:not([alt*=relative])[alt*=hm-tl] {
--image-adj-size-h: var(--med-tall);
}
:is(.view-content, .popover) img[alt][alt]:not([alt*=relative])[alt*=htall] {
--image-adj-size-h: var(--tall);
}
:is(.view-content, .popover) img[alt][alt]:not([alt*=relative])[alt*=hfull] {
--image-adj-size-h: 100%;
}
:is(.view-content, .popover) img[alt][alt]:not([alt*=relative])[alt*=wmicro] {
--image-adj-size-w: var(--micro);
}
:is(.view-content, .popover) img[alt][alt]:not([alt*=relative])[alt*=wtiny] {
--image-adj-size-w: var(--tiny);
}
:is(.view-content, .popover) img[alt][alt]:not([alt*=relative])[alt*=wsmall] {
--image-adj-size-w: var(--small);
}
:is(.view-content, .popover) img[alt][alt]:not([alt*=relative])[alt*=ws-med] {
--image-adj-size-w: var(--small-med);
}
:is(.view-content, .popover) img[alt][alt]:not([alt*=relative])[alt*=wm-sm] {
--image-adj-size-w: var(--med-small);
}
:is(.view-content, .popover) img[alt][alt]:not([alt*=relative])[alt*=wmed] {
--image-adj-size-w: var(--medium);
}
:is(.view-content, .popover) img[alt][alt]:not([alt*=relative])[alt*=wm-tl] {
--image-adj-size-w: var(--med-tall);
}
:is(.view-content, .popover) img[alt][alt]:not([alt*=relative])[alt*=wtall] {
--image-adj-size-w: var(--tall);
}
:is(.view-content, .popover) img[alt][alt]:not([alt*=relative])[alt*=wfull] {
--image-adj-size-w: 100%;
}
.image-embed[alt][alt*=relative],
div:not(.image-embed) > img[alt][alt*=relative] {
--micro: 10%;
--tiny: 20%;
--small: 30%;
--small-med: 40%;
--med-small: 50%;
--medium: 60%;
--med-tall: 70%;
--tall: 85%;
}
.image-embed[alt][alt*=relative][alt*=wmicro],
div:not(.image-embed) > img[alt][alt*=relative][alt*=wmicro] {
width: var(--micro);
}
.image-embed[alt][alt*=relative][alt*=wtiny],
div:not(.image-embed) > img[alt][alt*=relative][alt*=wtiny] {
width: var(--tiny);
}
.image-embed[alt][alt*=relative][alt*=wsmall],
div:not(.image-embed) > img[alt][alt*=relative][alt*=wsmall] {
width: var(--small);
}
.image-embed[alt][alt*=relative][alt*=ws-med],
div:not(.image-embed) > img[alt][alt*=relative][alt*=ws-med] {
width: var(--small-med);
}
.image-embed[alt][alt*=relative][alt*=wm-sm],
div:not(.image-embed) > img[alt][alt*=relative][alt*=wm-sm] {
width: var(--med-small);
}
.image-embed[alt][alt*=relative][alt*=wmed],
div:not(.image-embed) > img[alt][alt*=relative][alt*=wmed] {
width: var(--medium);
}
.image-embed[alt][alt*=relative][alt*=wm-tl],
div:not(.image-embed) > img[alt][alt*=relative][alt*=wm-tl] {
width: var(--med-tall);
}
.image-embed[alt][alt*=relative][alt*=wtall],
div:not(.image-embed) > img[alt][alt*=relative][alt*=wtall] {
width: var(--tall);
}
.image-embed[alt][alt*=relative][alt*=hmicro],
div:not(.image-embed) > img[alt][alt*=relative][alt*=hmicro] {
width: var(--micro);
}
.image-embed[alt][alt*=relative][alt*=htiny],
div:not(.image-embed) > img[alt][alt*=relative][alt*=htiny] {
width: var(--tiny);
}
.image-embed[alt][alt*=relative][alt*=hsmall],
div:not(.image-embed) > img[alt][alt*=relative][alt*=hsmall] {
width: var(--small);
}
.image-embed[alt][alt*=relative][alt*=hs-med],
div:not(.image-embed) > img[alt][alt*=relative][alt*=hs-med] {
width: var(--small-med);
}
.image-embed[alt][alt*=relative][alt*=hm-sm],
div:not(.image-embed) > img[alt][alt*=relative][alt*=hm-sm] {
width: var(--med-small);
}
.image-embed[alt][alt*=relative][alt*=hmed],
div:not(.image-embed) > img[alt][alt*=relative][alt*=hmed] {
width: var(--medium);
}
.image-embed[alt][alt*=relative][alt*=hm-tl],
div:not(.image-embed) > img[alt][alt*=relative][alt*=hm-tl] {
width: var(--med-tall);
}
.image-embed[alt][alt*=relative][alt*=htall],
div:not(.image-embed) > img[alt][alt*=relative][alt*=htall] {
width: var(--tall);
}
.image-embed[alt][alt*=relative][alt*=hfull],
div:not(.image-embed) > img[alt][alt*=relative][alt*=hfull] {
width: 100%;
}
.image-embed[alt][alt*=relative],
div:not(.image-embed) > img[alt][alt*=relative] {
display: block;
margin: auto;
max-height: 100%;
object-fit: cover;
}
/*Height*/
/*Image Locations*/
/*Center Image*/
.img-adj-center.img-adj-center img,
img:is([alt~=ctr], [alt~=center]) {
display: block;
margin-left: auto;
margin-right: auto;
}
.img-adj-center.img-adj-center .is-live-preview img {
margin-left: auto !important;
margin-right: auto !important;
}
/*Left & Right*/
.markdown-rendered img:is([alt~=left], [alt~=locl]), .markdown-rendered img:is([src*="#left"], [src*="#locl"]), .markdown-rendered .image-embed:is([alt~=left], [alt~=locl]), .markdown-rendered .image-embed:is([src*="#left"], [src*="#locl"]) {
float: left;
margin-right: 2%;
margin-top: 0px;
margin-bottom: 0px;
float: inline-start;
}
.markdown-rendered img:is([alt~=right], [alt~=locr]), .markdown-rendered img:is([src*="#right"], [src*="#locr"]), .markdown-rendered .image-embed:is([alt~=right], [alt~=locr]), .markdown-rendered .image-embed:is([src*="#right"], [src*="#locr"]) {
float: right;
margin-left: 2%;
margin-bottom: 0px;
float: inline-end;
}
/*--Image Position--*/
img[alt*="p+"], .image-embed[src*="#p+"] img {
object-fit: cover;
}
/*Inner Image*/
img[alt*="p+c"], .image-embed[src*="#p+c"] img {
object-position: center;
}
img[alt*="p+t"], .image-embed[src*="#p+t"] img {
object-position: top;
}
img[alt*="p+b"], .image-embed[src*="#p+b"] img {
object-position: bottom;
}
img[alt*="p+l"], .image-embed[src*="#p+l"] img {
object-position: left;
}
img[alt*="p+r"], .image-embed[src*="#p+r"] img {
object-position: right;
}
img[alt*="p+cl"], .image-embed[src*="#p+cl"] img {
object-position: 15%;
}
img[alt*="p+ccl"], .image-embed[src*="#p+ccl"] img {
object-position: 25%;
}
img[alt*="p+cr"], .image-embed[src*="#p+cr"] img {
object-position: 60%;
}
img[alt*="p+ccr"], .image-embed[src*="#p+ccr"] img {
object-position: 75%;
}
img[alt*="p+tc"], .image-embed[src*="#p+tc"] img {
object-position: 50% 10%;
}
img[alt*="p+tcc"], .image-embed[src*="#p+tcc"] img {
object-position: 50% 20%;
}
img[alt*="p+cct"], .image-embed[src*="#p+cct"] img {
object-position: 50% 30%;
}
img[alt*="p+ct"], .image-embed[src*="#p+ct"] img {
object-position: 50% 40%;
}
img[alt*="p+cb"], .image-embed[src*="#p+cb"] img {
object-position: 50% 60%;
}
img[alt*="p+ccb"], .image-embed[src*="#p+ccb"] img {
object-position: 50% 70%;
}
img[alt*="p+bc"], .image-embed[src*="#p+bc"] img {
object-position: 50% 80%;
}
img[alt*="p+bcc"], .image-embed[src*="#p+bcc"] img {
object-position: 50% 90%;
}
/*Invert Colors*/
.theme-dark img[alt*=invertb], .theme-dark .image-embed[src*="#invertb"] {
filter: invert(1) hue-rotate(180deg);
}
.theme-dark img[alt*=invertbc],
.theme-dark .image-embed[src*="#invertbc"] {
filter: invert(1) hue-rotate(180deg) contrast(1.5);
}
.theme-light img[alt*=invertw], .theme-light .image-embed[src*="#invertw"] {
filter: invert(1) hue-rotate(180deg);
}
.theme-light img[alt*=invertwc], .theme-light .image-embed[src*="#invertwc"] {
filter: invert(1) hue-rotate(180deg) contrast(1.45);
}
img:is([alt*=flip-x],
[alt*=flip-horizontal]) {
transform: scale(-1, 1);
}
img:is([alt*=flip-y],
[alt*=flip-vertical]) {
transform: scale(1, -1);
}
img:is([alt*=flip-xy],
[alt*=flip-vertical-horizontal]) {
transform: scale(-1, -1);
}
/*Fit image within bounds WITHOUT stretching*/
img[alt*=cover],
img:is([alt*=cover], [alt*=cvr]),
.image-embed:is([src*="#cover"], [src*="#cvr"]),
span.image-embed:is([src*="#cover"], [src*="#cvr"]) img {
object-fit: cover;
}
/*Fix Float Issues*/
:is(img, .image-embed)[alt*=clear],
.image-embed[src*="#clear"] {
clear: both;
}
img[alt*=unclr],
.image-embed[src*="#unclr"] {
clear: none !important;
}
img:is([alt~=lp], [alt~=live-preview]):is([alt*=right], [alt*=locr]),
.image-embed:is([alt~=lp], [alt~=live-preview]):is([alt*=right], [alt*=locr]) {
float: right !important;
}
img:is([alt~=lp], [alt~=live-preview]):is([alt*=left], [alt*=locl]),
.image-embed:is([alt~=lp], [alt~=live-preview]):is([alt*=left], [alt*=locl]) {
float: left !important;
}
.clear-hr {
--hr-width: 100%;
}
.clear-headings :is(h1, h2, h3, h4, h5, h6),
.clear-heading-1 h1,
.clear-heading-2 h2,
.clear-heading-3 h3,
.clear-heading-4 h4,
.clear-heading-5 h5,
.clear-heading-6 h6 {
clear: both;
}
/*Banners*/
img[alt*=banner]:not([width]),
.image-embed[alt*=banner]:not([width]) img {
display: block;
object-fit: cover;
width: 100%;
margin-bottom: 0px;
clear: both;
}
img[alt~=banner],
.image-embed[alt~=banner] img,
.image-embed[src*="#banner"] {
height: var(--small);
}
img[alt~="banner+small"],
.image-embed[alt~="banner+small"] img,
.image-embed[src*="#banner+small"] {
height: var(--tiny);
}
img[alt~="banner+tall"],
.image-embed[alt~="banner+tall"] img,
.image-embed[src*="#banner+tall"] {
height: var(--medium);
}
:is(img, .internal-embed)[alt*=sban],
:is(img, .internal-embed)[alt~=sban],
.internal-embed[src*="#sban"] img {
object-fit: cover;
width: 100%;
}
/*Portait*/
img[alt*=portrait],
.image-embed[alt*=portrait] img {
object-fit: cover;
}
.image-embed[src~="#portrait"] {
height: var(--small-med);
width: 40%;
}
.image-embed[src~="#portrait+small"] {
height: var(--small);
width: 25%;
}
.image-embed[src~="#portrait+tall"] {
height: 500px;
width: 50%;
}
img:is([alt~=portrait],
[alt*="portrait+"]),
.image-embed:is([alt~=portrait],
[alt*="portrait+"]) img {
--img-adj-portrait-size: var(--med-small);
height: var(--img-adj-portrait-size);
width: calc(var(--img-adj-portrait-size) / 1.7);
}
img[alt~="portrait+small"],
.image-embed[alt~="portrait+small"] img {
--img-adj-portrait-size: var(--small-med);
}
img[alt~="portrait+tall"],
.image-embed[alt~="portrait+tall"] img {
--img-adj-portrait-size: var(--medium);
}
/*Profile*/
img[alt*=profile],
.image-embed[alt*=profile] img {
object-fit: cover;
border-radius: 50%;
}
img[alt~=profile],
.image-embed[alt~=profile] img,
.image-embed[src*="#profile"] {
height: var(--tiny);
width: var(--tiny);
}
img[alt~="profile+medium"],
.image-embed[alt~="profile+medium"] img,
.image-embed[src*="#profile+medium"] {
height: var(--small);
width: var(--small);
}
img[alt~="profile+tall"],
.image-embed[alt~="profile+tall"] img,
.image-embed[src*="#profile+tall"] {
height: var(--medium);
width: var(--medium);
}
img[alt~=sprf] {
object-fit: cover;
border-radius: 100%;
}
/*Image Shapes*/
img[alt][alt*=circle] {
border-radius: 50%;
}
img[alt~=square],
.image-embed[alt~=square] img {
border-radius: 0;
}
img[alt~=border],
.internal-embed[alt~=border] img {
border: var(--image-border-width) solid var(--image-border-color);
padding: var(--image-border-padding);
background: var(--image-border-background);
}
.image-captions .image-embed::after,
.image-embed[src*="#cap"]::after {
content: attr(alt);
color: var(--inactive, var(--faint-text));
display: block;
text-align: center;
}
.image-embed[src*="#cap"] {
display: inline-block;
}
.image-embed[src*="#cap"] img {
float: unset !important;
object-fit: cover;
}
.image-embed[src*="#cap"][src*="#hmicro"] img {
height: var(--micro);
}
.image-embed[src*="#cap"][src*="#htiny"] img {
height: var(--tiny);
}
.image-embed[src*="#cap"][src*="#hsmall"] img {
height: var(--small);
}
.image-embed[src*="#cap"][src*="#hs-med"] img {
height: var(--small-med);
}
.image-embed[src*="#cap"][src*="#hm-sm"] img {
height: var(--med-small);
}
.image-embed[src*="#cap"][src*="#hmed"] img {
height: var(--medium);
}
.image-embed[src*="#cap"][src*="#hm-tl"] img {
height: var(--med-tall);
}
.image-embed[src*="#cap"][src*="#htall"] img {
height: var(--tall);
}
.image-embed[src*="#cap"][src*="#hfull"] img {
height: 100%;
}
.image-embed[src*="#cap"][src*="#wmicro"], .image-embed[src*="#cap"][src*="#wmicro"] img {
width: var(--micro);
}
.image-embed[src*="#cap"][src*="#wtiny"], .image-embed[src*="#cap"][src*="#wtiny"] img {
width: var(--tiny);
}
.image-embed[src*="#cap"][src*="#wsmall"], .image-embed[src*="#cap"][src*="#wsmall"] img {
width: var(--small);
}
.image-embed[src*="#cap"][src*="#ws-med"], .image-embed[src*="#cap"][src*="#ws-med"] img {
width: var(--small-med);
}
.image-embed[src*="#cap"][src*="#wm-sm"], .image-embed[src*="#cap"][src*="#wm-sm"] img {
width: var(--med-small);
}
.image-embed[src*="#cap"][src*="#wmed"], .image-embed[src*="#cap"][src*="#wmed"] img {
width: var(--medium);
}
.image-embed[src*="#cap"][src*="#wm-tl"], .image-embed[src*="#cap"][src*="#wm-tl"] img {
width: var(--med-tall);
}
.image-embed[src*="#cap"][src*="#wtall"], .image-embed[src*="#cap"][src*="#wtall"] img {
width: var(--tall);
}
.image-embed[src*="#cap"][src*="#wfull"], .image-embed[src*="#cap"][src*="#wfull"] img {
width: 100%;
}
.mobile-image-viewer img[alt][alt][alt] {
height: 100%;
width: 100%;
object-fit: contain;
}
/*@settings
name: Image Adjustments
id: image-adjustments
settings:
-
id: info-text-SlRvb-img-adj
type: info-text
title: Image Adjustments by SlRvb
description: "[Image Adjustments Snippet How-To Guide](https://publish.obsidian.md/slrvb-docs/ITS+Theme/Image+Adjustments)"
markdown: true
-
title: List Overlap Fix
description: Fix list bullets overlapping with images
id: img-adj-list
type: class-toggle
default: true
-
title: Clear Images
description: Push image under/over headings or horizontal lines
id: img-adj-clears
type: heading
level: 1
collapsed: true
-
title: Horizontal Lines
description: Push image under/over any horizontal lines
id: clear-hr
type: class-toggle
-
title: Headings
description: Push image under/over all headings 1-6
id: clear-headings
type: class-toggle
-
title: Heading Specific
description: Push image under/over some headings and not others
id: img-adj-clears-headings
type: heading
level: 2
collapsed: true
-
title: Header 1
id: clear-heading-1
type: class-toggle
-
title: Header 2
id: clear-heading-2
type: class-toggle
-
title: Header 3
id: clear-heading-3
type: class-toggle
-
title: Header 4
id: clear-heading-4
type: class-toggle
-
title: Header 5
id: clear-heading-5
type: class-toggle
-
title: Header 6
id: clear-heading-6
type: class-toggle
*/
/*Theme fixes*/
.img-adj-list :is(ul, ol) {
display: flow-root;
}
.obsidian/snippets/vault-colors.css
Vendored
+60
View File
@@ -0,0 +1,60 @@
/* ============================================================
claude-obsidian vault colors
3-color scheme: blue (knowledge) | green (content) | purple (people)
============================================================ */
:root {
--cb-blue: #4fc1ff; /* concepts, domains — knowledge nodes */
--cb-green: #6a9955; /* sources, questions — content nodes */
--cb-purple: #c586c0; /* entities — people & orgs */
--cb-meta: #569cd6; /* wiki meta: index, hot, log */
--cb-dim: #606060; /* templates, raw — de-emphasized */
}
/* ── Wiki meta (light blue) ── */
.nav-folder-title[data-path="wiki"] { color: var(--cb-meta); }
.nav-folder-title[data-path^="wiki/meta"] { color: var(--cb-meta); }
/* ── Knowledge — blue ── */
.nav-folder-title[data-path^="wiki/concepts"] { color: var(--cb-blue); }
.nav-folder-title[data-path^="wiki/domains"] { color: var(--cb-blue); }
/* ── Content — green ── */
.nav-folder-title[data-path^="wiki/sources"] { color: var(--cb-green); }
.nav-folder-title[data-path^="wiki/questions"] { color: var(--cb-green); }
.nav-folder-title[data-path^="wiki/comparisons"] { color: var(--cb-green); }
/* ── People & orgs — purple ── */
.nav-folder-title[data-path^="wiki/entities"] { color: var(--cb-purple); }
/* ── De-emphasized ── */
.nav-folder-title[data-path=".raw"] { color: var(--cb-dim); opacity: 0.55; }
.nav-folder-title[data-path="_templates"] { color: var(--cb-dim); opacity: 0.55; }
.nav-folder-title[data-path="agents"] { color: var(--cb-dim); opacity: 0.55; }
.nav-folder-title[data-path="commands"] { color: var(--cb-dim); opacity: 0.55; }
.nav-folder-title[data-path="hooks"] { color: var(--cb-dim); opacity: 0.55; }
.nav-folder-title[data-path="skills"] { color: var(--cb-dim); opacity: 0.55; }
/* ── Custom callouts ── */
.callout[data-callout='contradiction'] {
--callout-color: 209, 105, 105;
--callout-icon: lucide-alert-triangle;
}
.callout[data-callout='gap'] {
--callout-color: 220, 220, 170;
--callout-icon: lucide-help-circle;
}
.callout[data-callout='key-insight'] {
--callout-color: 79, 193, 255;
--callout-icon: lucide-lightbulb;
}
.callout[data-callout='stale'] {
--callout-color: 128, 128, 128;
--callout-icon: lucide-clock;
}
/* ── Canvas card accents (match graph node colors) ── */
.canvas-node[data-color="1"] { --canvas-color: 79, 193, 255; } /* blue */
.canvas-node[data-color="3"] { --canvas-color: 197, 134, 192; } /* purple */
.canvas-node[data-color="4"] { --canvas-color: 106, 153, 85; } /* green */
.canvas-node[data-color="5"] { --canvas-color: 86, 156, 214; } /* meta */
.obsidian/workspace.json
Vendored
+43 -58
View File
@@ -1,40 +1,20 @@
{
"main": {
"id": "b33042e1dae2ebee",
"id": "cb698273c33e48de",
"type": "split",
"children": [
{
"id": "d6adc6f6ab929fb8",
"id": "477f1cf965ca606e",
"type": "tabs",
"children": [
{
"id": "11878edbbb5f0b0a",
"type": "leaf",
"state": {
"type": "markdown",
"state": {
"file": "환영합니다!.md",
"mode": "source",
"source": false
},
"icon": "lucide-file",
"title": "환영합니다!"
}
}
]
},
{
"id": "9a59b699c2664d6e",
"type": "tabs",
"children": [
{
"id": "1e6a9de3e7a2f91f",
"id": "a31de1b302cdc5cf",
"type": "leaf",
"state": {
"type": "graph",
"state": {},
"icon": "lucide-git-fork",
"title": "그래프 뷰"
"title": "Graph view"
}
}
]
@@ -43,15 +23,15 @@
"direction": "vertical"
},
"left": {
"id": "9345f240ecf9718f",
"id": "db8d83ac47ae599f",
"type": "split",
"children": [
{
"id": "91216e15c89884c5",
"id": "554fd2b4fa6f8741",
"type": "tabs",
"children": [
{
"id": "a334448a82082dfb",
"id": "5565f1231fe95c42",
"type": "leaf",
"state": {
"type": "file-explorer",
@@ -60,11 +40,11 @@
"autoReveal": false
},
"icon": "lucide-folder-closed",
"title": "파일 탐색기"
"title": "Files"
}
},
{
"id": "3fde83500b942e71",
"id": "832ab43d08cf9e30",
"type": "leaf",
"state": {
"type": "search",
@@ -77,17 +57,17 @@
"sortOrder": "alphabetical"
},
"icon": "lucide-search",
"title": "검색"
"title": "Search"
}
},
{
"id": "37b12a15d0fa6468",
"id": "097e8347bb8aa054",
"type": "leaf",
"state": {
"type": "bookmarks",
"state": {},
"icon": "lucide-bookmark",
"title": "북마크"
"title": "Bookmarks"
}
}
]
@@ -97,20 +77,19 @@
"width": 300
},
"right": {
"id": "b319432f1125be96",
"id": "7092b65be1e76349",
"type": "split",
"children": [
{
"id": "400f9cd61e8ce9b1",
"id": "9f4de9402eae371b",
"type": "tabs",
"children": [
{
"id": "bde996f9da69c71a",
"id": "a32b7215b7814fbb",
"type": "leaf",
"state": {
"type": "backlink",
"state": {
"file": "환영합니다!.md",
"collapseAll": false,
"extraContext": false,
"sortOrder": "alphabetical",
@@ -120,25 +99,24 @@
"unlinkedCollapsed": true
},
"icon": "links-coming-in",
"title": "환영합니다! 의 백링크"
"title": "Backlinks"
}
},
{
"id": "db2dbfd8d9544d44",
"id": "7936f8ba26007091",
"type": "leaf",
"state": {
"type": "outgoing-link",
"state": {
"file": "환영합니다!.md",
"linksCollapsed": false,
"unlinkedCollapsed": true
},
"icon": "links-going-out",
"title": "환영합니다! 의 나가는 링크"
"title": "Outgoing links"
}
},
{
"id": "364cc9b1930534f7",
"id": "ed8ccb323a603d61",
"type": "leaf",
"state": {
"type": "tag",
@@ -149,11 +127,11 @@
"searchQuery": ""
},
"icon": "lucide-tags",
"title": "태그"
"title": "Tags"
}
},
{
"id": "7e1c14ddf85167c6",
"id": "b140a331162907cf",
"type": "leaf",
"state": {
"type": "all-properties",
@@ -163,22 +141,31 @@
"searchQuery": ""
},
"icon": "lucide-archive",
"title": "모든 속성"
"title": "All properties"
}
},
{
"id": "ba5f9cca95ba7d37",
"id": "111a21e12ab1a293",
"type": "leaf",
"state": {
"type": "outline",
"state": {
"file": "환영합니다!.md",
"followCursor": false,
"showSearch": false,
"searchQuery": ""
},
"icon": "lucide-list",
"title": "환영합니다! 의 개요"
"title": "Outline"
}
},
{
"id": "20a272e103b5d792",
"type": "leaf",
"state": {
"type": "calendar",
"state": {},
"icon": "lucide-ghost",
"title": "calendar"
}
}
]
@@ -190,17 +177,15 @@
},
"left-ribbon": {
"hiddenItems": {
"switcher:빠른 전환기 열기": false,
"graph:그래프 뷰 열기": false,
"canvas:새 캔버스 만들기": false,
"daily-notes:오늘의 일일 노트 열기": false,
"templates:템플릿 삽입": false,
"command-palette:명령어 팔레트 열기": false,
"bases:새 베이스 생성하기": false
"switcher:Open quick switcher": false,
"graph:Open graph view": false,
"canvas:Create new canvas": false,
"daily-notes:Open today's daily note": false,
"templates:Insert template": false,
"command-palette:Open command palette": false,
"bases:Create new base": false
}
},
"active": "11878edbbb5f0b0a",
"lastOpenFiles": [
"환영합니다!.md"
]
"active": "a31de1b302cdc5cf",
"lastOpenFiles": []
}
.raw/.gitkeep
View File
.raw/.manifest.json
+9
View File
@@ -0,0 +1,9 @@
{
"version": 1,
"created": "2026-04-23",
"description": "Ingest delta tracker and address map for the claude-obsidian vault. Do not hand-edit; wiki-ingest maintains this.",
"sources": {},
"address_map": {
"wiki/concepts/DragonScale Memory.md": "c-000001"
}
}
.raw/claude-obsidian-ecosystem-research.md
+288
View File
@@ -0,0 +1,288 @@
---
type: raw-research
title: "Claude + Obsidian Ecosystem Research"
date: 2026-04-08
queries:
- "claude obsidian plugin github 2025 2026"
- "obsidian MCP server claude anthropic"
- "claudesidian obsidian plugin github"
- "obsidian smart connections copilot AI plugin"
- "claude code obsidian workflow LLM wiki"
sources:
- github.com
- awesome.ecosyste.ms
- obsidianstats.com
- effortlessacademic.com
---
# Claude + Obsidian Ecosystem Research
> Researched: 2026-04-08 | Goal: survey the Claude + Obsidian ecosystem and identify strong patterns and prior art relevant to claude-obsidian.
---
## Summary
16+ active projects found combining Claude/AI with Obsidian. Organized into 4 categories:
1. **LLM Wiki Pattern plugins** (Claude Code skill-based, closest in approach)
2. **Native Obsidian plugins** (TypeScript, embedded UI)
3. **MCP servers** (bridge protocols)
4. **In-vault AI plugins** (traditional Obsidian community plugins)
---
## Category 1: LLM Wiki Pattern (Claude Code Plugins)
### AgriciDaniel/claude-obsidian (this project)
- URL: https://github.com/AgriciDaniel/claude-obsidian
- Version: 1.2.0
- Skills: /wiki, /wiki-ingest, /wiki-query, /wiki-lint, /save, /autoresearch, /canvas
- Approach: Hot cache + compounding wiki + Claude Code skills
### heyitsnoah/claudesidian
- URL: https://github.com/heyitsnoah/claudesidian
- Approach: Pre-configured Obsidian vault + PARA method
- Key features:
- `/init-bootstrap` — interactive setup wizard that analyzes existing vault
- Vault import: safely imports existing vault to `OLD_VAULT/`
- Research public work to personalize context
- Thinking Mode vs Writing Mode distinction
- Pre-configured commands: `/thinking-partner`, `/daily-review`, `/research-assistant`, `/weekly-synthesis`, `/inbox-processor`
- PARA folder structure: 00_Inbox, 01_Projects, 02_Areas, 03_Resources, 04_Archive
- Optional: Gemini Vision for image/video, Firecrawl for web research
- Stars: Not tracked (pre-release kit)
### rvk7895/llm-knowledge-bases
- URL: https://github.com/rvk7895/llm-knowledge-bases
- Install: `/plugin marketplace add rvk7895/llm-knowledge-bases`
- Key features:
- 3-depth query system: Quick (indexes only), Standard (wiki + web search), Deep (multi-agent parallel web search)
- `/research` and `/research-deep` — parallel agents for deep research
- Output formats: Markdown reports, Marp slides, matplotlib charts → `output/`
- X/Twitter ingestion via Smaug tool
- `/kb-init`, `/kb compile`, `/kb query`, `/kb lint`, `/kb evolve`
- Attribution: Built on Karpathy pattern + Weizhena's Deep Research skills
### ekadetov/llm-wiki
- URL: https://github.com/ekadetov/llm-wiki
- Key features:
- qmd hybrid search (BM25 + vector) — auto-installed via SessionStart hook
- Multi-wiki support: `/llm-wiki:wiki init <topic-name>` creates isolated wiki
- URL ingestion: pass `https://` URLs directly to ingest command
- Auto-commit on every ingest via git
- Marp presentation output
- `/llm-wiki:wiki remove <topic>` — clean removal
- Prerequisite: Node 18+, Git, Obsidian vault at `~/ObsidianVault/`
### Ar9av/obsidian-wiki
- URL: https://github.com/Ar9av/obsidian-wiki
- Key features:
- Multi-agent compatibility: Claude Code, Cursor, Windsurf, Codex, Gemini CLI, OpenClaw, GitHub Copilot
- `setup.sh` auto-configures all agents simultaneously via symlinks
- Delta tracking manifest (`.manifest.json`) — only ingests new/changed files
- Vision support: ingest images, screenshots, whiteboard photos (requires vision model)
- 4-stage pipeline: Ingest → Extract → Resolve → Schema
- Schema emerges from sources (not fixed upfront)
- Each page gets `summary:` frontmatter for preview without opening
- Multi-format: PDFs (with page ranges), JSONL, conversation exports, transcripts
### ballred/obsidian-claude-pkm
- URL: https://github.com/ballred/obsidian-claude-pkm
- Key features:
- Goal cascade: 3-Year Vision → Yearly Goals → Projects → Monthly Goals → Weekly Review → Daily Tasks
- `/daily`, `/weekly`, `/monthly` review skills
- `/project new` — creates project linked to a goal
- `/adopt` command — imports existing vault structure, detects PARA/Zettelkasten/LYT, maps folders
- 4 specialized agents: goal-aligner, weekly-reviewer, note-organizer, inbox-processor
- `memory: project` for cross-session agent learning
- Auto-commit via PostToolUse hook on every file write/edit
- Productivity Coach output style
- Path-specific rules loaded contextually
- Zero dependencies (bash + markdown only)
- `/onboard` — personalized vault setup (name, review day, goal areas)
- Version: 3.1
### kepano/obsidian-skills
- URL: https://github.com/kepano/obsidian-skills
- Author: **Linus Kepano** (creator of Obsidian + Minimal theme)
- Install: `/plugin marketplace add kepano/obsidian-skills`
- Key skills:
- `obsidian-markdown` — full Obsidian Flavored Markdown (callouts, embeds, wikilinks, properties)
- `obsidian-bases` — Obsidian Bases (.base files, views, filters, formulas)
- `json-canvas` — JSON Canvas spec for .canvas files
- `obsidian-cli` — vault management via Obsidian CLI
- `defuddle` — extract clean markdown from web pages (removes clutter, saves tokens)
- Multi-platform: Claude Code, Codex CLI, OpenCode
### ussumant/llm-wiki-compiler
- URL: https://github.com/ussumant/llm-wiki-compiler
- Approach: Single-purpose Claude Code plugin — compiles markdown files into topic wiki
- Key features: Topic-based compilation, implements Karpathy pattern in minimal form
---
## Category 2: Native Obsidian Plugins (Embedded UI)
### YishenTu/claudian
- URL: https://github.com/YishenTu/claudian
- Approach: Embeds Claude Code/Codex CLI directly inside Obsidian as sidebar chat
- Key features:
- **Inline Edit** — select text + hotkey → word-level diff preview → apply
- **Plan Mode** (Shift+Tab) — agent plans before implementing
- **@mention** — reference vault files, subagents, MCP servers, external files
- **Slash commands & Skills** — user- and vault-level skill scopes
- **Instruction Mode (#)** — add instructions from chat input
- **MCP Servers** — stdio, SSE, HTTP connections
- **Multi-tab conversations** — fork, resume, compact
- Privacy: no telemetry, stores in vault/.claudian/
- Requires BRAT or manual install (not yet in community store)
### ProfSynapse/claudesidian-mcp (now: Nexus)
- URL: https://github.com/ProfSynapse/claudesidian-mcp
- Current name: Nexus MCP for Obsidian
- Approach: Full Obsidian plugin with both native chat AND MCP bridge
- Key features:
- Native chat inside Obsidian (any provider via settings)
- MCP bridge for: Claude Desktop, Claude Code, Codex CLI, Gemini CLI, Cursor, Cline
- **Workspace memory** — persistent context across sessions (JSONL, Obsidian Sync compatible)
- **Task management** — projects, tasks, blockers, dependencies
- **Semantic search** — search notes + past conversations by meaning
- **Inline editing** — edit selected text in notes
- PDF + audio → Markdown conversion (right-click or auto-on-add)
- Web page → Markdown/PNG/PDF capture
- Merge PDFs, concat markdown, mix audio tracks
- Mobile support (native chat)
- Storage: JSONL files in `.obsidian/plugins/nexus/data/` (included in Obsidian Sync)
- Two-tool architecture (see docs)
---
## Category 3: MCP Servers
### jacksteamdev/obsidian-mcp-tools
- URL: https://github.com/jacksteamdev/obsidian-mcp-tools
- Key features:
- Vault access via Local REST API plugin
- **Semantic search** via Smart Connections integration
- **Templater execution** — run templates from AI with dynamic params
- SLSA Level 3 binary attestation (reproducible, signed builds)
- Requires: Local REST API + Smart Connections + Templater
- Status: Seeking maintainers (open until Sep 2025)
### YuNaga224/obsidian-memory-mcp
- URL: https://github.com/YuNaga224/obsidian-memory-mcp
- Key features:
- Fork of Anthropic's official memory MCP server
- Stores AI memories as individual Markdown files (not JSON)
- Uses `[[link]]` syntax → entities appear in Obsidian graph view
- YAML frontmatter: entityType, created, updated
- Sections: Observations + Relations per entity
- Tools: create_entities, create_relations, add_observations, search_nodes, read_graph
- Configure via MEMORY_DIR env var pointing to vault folder
### iansinnott/obsidian-claude-code-mcp
- URL: https://github.com/iansinnott/obsidian-claude-code-mcp
- Key features: WebSocket-based MCP, auto-discovers Obsidian vaults via Claude Code
### administrativetrick/obsidian-mcp
- URL: https://github.com/administrativetrick/obsidian-mcp
- Minimal MCP server for Claude Desktop vault access
### dbmcco/obsidian-mcp
- URL: https://github.com/dbmcco/obsidian-mcp
- TDD-developed MCP server for Obsidian
### MarkusPfundstein/mcp-obsidian
- URL: https://github.com/MarkusPfundstein/mcp-obsidian
- Interacts via Obsidian REST API community plugin
---
## Category 4: Traditional In-Vault AI Plugins (Stars)
| Plugin | Stars | Feature |
|--------|-------|---------|
| logancyang/obsidian-copilot | 5,776 | Multi-provider AI chat with vault context |
| brianpetro/obsidian-smart-connections | 4,357 | Vector embeddings, semantic search, local models, Claude support |
| nhaouari/obsidian-textgenerator-plugin | 1,837 | Text generation |
| bramses/chatgpt-md | 1,229 | Chat in markdown |
| pfrankov/obsidian-local-gpt | 569 | Local LLM integration |
| infiolab/infio-copilot | unknown | Cursor-inspired: autocomplete, inline edit, workspaces, Insights, dataview queries |
| solderneer/obsidian-ai-tools | 272 | Semantic search via Supabase + OpenAI |
---
## Ecosystem Stats (danielrosehill/Awesome-Obsidian-AI-Tools)
- 86 plugins total, 19,737 combined stars
- 17 categories
- Last updated: 2025-12-15
---
## Key Design Patterns Across Ecosystem
### Pattern 1: Delta Tracking
Most mature projects (Ar9av/obsidian-wiki) use a `.manifest.json` to track ingested sources — hash, timestamp, which pages produced. Re-ingest only processes changed/new files. Claude-obsidian currently has no delta tracking.
### Pattern 2: Multi-Depth Queries
rvk7895 implements 3 tiers: Quick (index only), Standard (wiki + web), Deep (parallel agents). Current claude-obsidian has one depth level in wiki-query.
### Pattern 3: Goal Cascade Integration
ballred's project connects personal productivity (daily/weekly reviews) with the knowledge base. No PKM projects do this today in claude-obsidian.
### Pattern 4: Auto-Commit Hooks
ballred uses PostToolUse hooks for auto-git-commit on every file change. This keeps the vault in version control automatically.
### Pattern 5: Multi-Agent Compatibility
Ar9av's setup.sh deploys skills to Claude Code + Cursor + Windsurf + Codex + Gemini CLI simultaneously. claude-obsidian is Claude Code only.
### Pattern 6: Hybrid Search
ekadetov uses qmd (BM25 + vector) instead of simple keyword/index search. Big quality improvement for large vaults.
### Pattern 7: Emerging Schema
Ar9av's wiki has no fixed structure upfront — it emerges from the content. Claude-obsidian has a predefined structure.
### Pattern 8: Vision Ingestion
Ar9av supports images/screenshots/whiteboards as ingestable sources (vision model required). Claude-obsidian has no image ingestion.
### Pattern 9: Output Formats
rvk7895 and ekadetov export to Marp slides and matplotlib charts. Claude-obsidian outputs only Markdown.
### Pattern 10: Vault Adoption
Both claudesidian and ballred/pkm can be adopted onto existing vaults without destroying structure. Claude-obsidian requires starting fresh.
---
## Notable Quotes / Signal
From rvk7895 README:
> "The LLM owns the wiki. You rarely edit it manually — just explore in Obsidian and keep feeding it raw data."
From Ar9av README:
> "You write skills once, every agent can use them."
> "The wiki schema isn't fixed upfront. It emerges from your sources."
From kepano/obsidian-skills (Obsidian creator):
> Uses exact Agent Skills specification format — validates that AgriciDaniel's approach is on spec.
---
## Sources
- https://github.com/AgriciDaniel/claude-obsidian
- https://github.com/heyitsnoah/claudesidian
- https://github.com/ProfSynapse/claudesidian-mcp
- https://github.com/YishenTu/claudian
- https://github.com/kepano/obsidian-skills
- https://github.com/danielrosehill/Awesome-Obsidian-AI-Tools
- https://github.com/Ar9av/obsidian-wiki
- https://github.com/ekadetov/llm-wiki
- https://github.com/rvk7895/llm-knowledge-bases
- https://github.com/jacksteamdev/obsidian-mcp-tools
- https://github.com/ballred/obsidian-claude-pkm
- https://github.com/infiolab/infio-copilot
- https://github.com/YuNaga224/obsidian-memory-mcp
- https://github.com/iansinnott/obsidian-claude-code-mcp
- https://github.com/ussumant/llm-wiki-compiler
- https://github.com/logancyang/obsidian-copilot
- https://github.com/brianpetro/obsidian-smart-connections
- https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f
.vault-meta/address-counter.txt
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3
.vault-meta/legacy-pages.txt
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# DragonScale legacy-pages manifest
# rollout: 2026-04-23
#
# List, one path per line, any pages whose frontmatter `created:` date is
# post-rollout but which should still be treated as legacy (i.e. not required
# to have an address). Also lines beginning with "# rollout:" set the
# per-vault rollout baseline used by wiki-lint for severity classification.
# Example:
# wiki/sources/old-page-with-wrong-metadata.md
.vault-meta/locks/.gitkeep
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# Placeholder so .vault-meta/locks/ exists on fresh clone.
# Actual lock files are gitignored; this file is whitelisted in .gitignore.
# scripts/wiki-lock.sh ensure_dirs() also creates this directory at runtime
# if absent, but having it pre-created avoids first-acquire side-effect.
.vault-meta/tiling-thresholds.json
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{
"version": 1,
"model": "nomic-embed-text",
"bands": {
"error": 0.90,
"review": 0.80
},
"calibrated": false,
"calibration_pairs_labeled": 0,
"notes": "Conservative seed thresholds, NOT calibrated against this vault and NOT a literature-backed interpolation. Published reference points: Sentence Transformers community_detection defaults to 0.75; Quora-duplicate calibrations land around 0.7715-0.8352 for F1 and accuracy objectives. At 0.80 review floor, expect false negatives against those baselines. Replace with vault-calibrated bands when 50-100 labeled pairs are available. See wiki-lint SKILL.md Semantic Tiling section for the calibration procedure."
}
.windsurf/rules/claude-obsidian.md
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# claude-obsidian: Windsurf Rules
This repo is a knowledge companion that builds persistent, compounding Obsidian wiki vaults using Andrej Karpathy's LLM Wiki pattern. The skills are written in the cross-platform Agent Skills format and work in Cascade alongside Claude Code.
## Project Type
- **Hybrid**: Claude Code plugin + Obsidian vault
- **Pattern**: LLM Wiki (Karpathy)
- **Stack**: Markdown only: no build step, no runtime dependencies
## What's In This Repo
```
claude-obsidian/
├── skills/ ← 10 SKILL.md files (Agent Skills format)
├── hooks/ ← SessionStart, PostCompact, PostToolUse, Stop
├── .claude-plugin/ ← Claude Code plugin manifest
├── _templates/ ← Obsidian Templater templates
├── wiki/ ← Generated knowledge base
│ ├── hot.md ← recent context cache (~500 tokens)
│ ├── index.md ← master catalog
│ ├── log.md ← append-only operation log
│ ├── concepts/, entities/, sources/, comparisons/, questions/
│ └── meta/dashboard.base ← Obsidian Bases dashboard
└── .raw/ ← Immutable source documents
```
## Skills Available to Cascade
Run `bash bin/setup-multi-agent.sh` once to symlink `skills/` into `.windsurf/skills/`. Then Cascade auto-discovers all 10 skills:
- `wiki`: orchestration, vault scaffolding, hot cache
- `wiki-ingest`: files, URLs, images → 8-15 wiki pages
- `wiki-query`: Quick / Standard / Deep query modes
- `wiki-lint`: health check (orphans, dead links, gaps)
- `save`: file conversation as wiki note
- `autoresearch`: autonomous research loop
- `canvas`: Obsidian canvas (.canvas) files
- `defuddle`: clean web pages before ingest
- `obsidian-markdown`: full Obsidian syntax reference
- `obsidian-bases`: Obsidian Bases (.base) database views
## Critical Rules
- **Never modify `.raw/`**: those are source documents
- **Read `wiki/hot.md` silently at session start** to restore context
- **Use wikilinks** `[[Note Name]]` for all internal references
- **Frontmatter is flat YAML** with plural keys (`tags`, `aliases`)
- **Auto-commit hook** fires on every Write/Edit to `wiki/` and `.raw/`
- **Append to `wiki/log.md`** at the top, never edit past entries
## Bootstrap
When the user opens this project in Windsurf:
1. Read this rules file
2. If `wiki/hot.md` exists, silently read it
3. Wait for triggers like "set up wiki", "ingest", or "query"
## Links
- https://github.com/AgriciDaniel/claude-obsidian
- https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f
- https://github.com/kepano/obsidian-skills
AGENTS.md
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# claude-obsidian: Agent Instructions
This repo is a Claude Code plugin **and** an Obsidian vault that builds persistent, compounding knowledge bases using Andrej Karpathy's LLM Wiki pattern. It works with **any AI coding agent** that supports the Agent Skills standard, including Codex CLI, OpenCode, and similar.
Originally built for Claude Code, the skills follow the cross-platform Agent Skills spec. Newer skills (`wiki-fold`, `wiki-ingest`, `wiki-lint`) use only `name` and `description` frontmatter (kepano convention). Some older skills still carry an optional `allowed-tools` field for Claude Code compatibility; cross-platform agents that do not recognize it should ignore it.
## Skills Discovery
All skills live in `skills/<name>/SKILL.md`. Codex / OpenCode / other Agent Skills compatible agents will auto-discover them when you symlink the directory:
```bash
# Codex CLI
ln -s "$(pwd)/skills" ~/.codex/skills/claude-obsidian
# OpenCode
ln -s "$(pwd)/skills" ~/.opencode/skills/claude-obsidian
```
Or run the bundled installer:
```bash
bash bin/setup-multi-agent.sh
```
## Available Skills
| Skill | Trigger phrases |
|---|---|
| `wiki` | `/wiki`, set up wiki, scaffold vault |
| `wiki-ingest` | ingest, ingest this url, ingest this image, batch ingest |
| `wiki-query` | query, what do you know about, query quick:, query deep: |
| `wiki-lint` | lint the wiki, health check, find orphans |
| `wiki-fold` | fold the log, run a fold, log rollup (DragonScale Mechanism 1, opt-in) |
| `save` | /save, file this conversation |
| `autoresearch` | autoresearch, autonomous research loop |
| `canvas` | /canvas, add to canvas, create canvas |
| `defuddle` | clean this url, defuddle |
| `obsidian-markdown` | obsidian syntax, wikilink, callout |
| `obsidian-bases` | obsidian bases, .base file, dynamic table |
## Key Conventions
- **Vault root**: the directory containing `wiki/` and `.raw/`
- **Hot cache**: `wiki/hot.md` (read at session start, updated at session end)
- **Source documents**: `.raw/` (immutable: agents never modify these)
- **Generated knowledge**: `wiki/` (agent-owned, links to sources via wikilinks)
- **Manifest**: `.raw/.manifest.json` tracks ingested sources (delta tracking)
## Bootstrap
When the user opens this project for the first time:
1. Read this file (`AGENTS.md`) and the project `CLAUDE.md` for full context
2. Read `skills/wiki/SKILL.md` for the orchestration pattern
3. If `wiki/hot.md` exists, read it silently to restore recent context
4. If the user types `/wiki` (or "set up wiki"), follow the wiki skill's scaffold workflow
## Reference
- Plugin homepage (public canonical): https://github.com/AgriciDaniel/claude-obsidian
- Community early-access mirror (Pro): https://github.com/AI-Marketing-Hub
- Pattern source: https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f
- Cross-reference: https://github.com/kepano/obsidian-skills (authoritative Obsidian-specific skills)
ATTRIBUTION.md
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# Attributions
claude-obsidian is an original work. The following third-party patterns, tools, and creators informed its design.
---
## LLM Wiki Pattern
**Author:** Andrej Karpathy
**Source:** https://github.com/karpathy
**Use:** The core architecture of claude-obsidian — using an LLM to build and maintain a structured wiki from raw sources — is based on the LLM Wiki pattern Karpathy described publicly. claude-obsidian is an independent implementation; no code or content from Karpathy's repositories was copied.
---
## ITS CSS Snippets
**Author:** SlRvb
**Source:** https://github.com/SlRvb/Obsidian--ITS-Theme
**License:** GPL-2.0
**Files:**
- `.obsidian/snippets/ITS-Dataview-Cards.css`
- `.obsidian/snippets/ITS-Image-Adjustments.css`
These snippets are distributed under the GPL-2.0 license. Per GPL-2.0 terms, any modifications to these files must also be released under GPL-2.0.
---
## Obsidian Plugins (pre-installed)
The following Obsidian community plugins ship with this vault as pre-installed binaries. They are the property of their respective authors and are distributed here solely to reduce setup friction. Users should verify license terms via each plugin's repository.
| Plugin | Author | Repository |
|--------|--------|-----------|
| Calendar | Liam Cain | https://github.com/liamcain/obsidian-calendar-plugin |
| Thino | Boninall (Quorafind) | https://github.com/Quorafind/Obsidian-Thino |
| Obsidian Excalidraw | Zsolt Viczian | https://github.com/zsviczian/obsidian-excalidraw-plugin |
| Obsidian Banners | Danny Hernandez | https://github.com/noatpad/obsidian-banners |
`obsidian-excalidraw-plugin/main.js` is **not** included in this repository. It is downloaded automatically by `bin/setup-vault.sh` from the plugin's official GitHub releases.
---
## claude-obsidian
**Author:** AgriciDaniel / AI Marketing Hub
**License:** MIT (see [LICENSE](LICENSE))
**Repository (public canonical):** https://github.com/AgriciDaniel/claude-obsidian
**Community early-access mirror (Pro):** https://github.com/AI-Marketing-Hub
CHANGELOG.md
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# Changelog
All notable changes to claude-obsidian. Format: [Keep a Changelog](https://keepachangelog.com/en/1.1.0/). Versioning: [SemVer](https://semver.org/).
## [1.9.2] - 2026-05-27 (prompt-cache hardening + path-handling robustness)
Ports Anthropic prompt-caching best practices into the **one** place the plugin calls the Anthropic API directly: tier-1 contextual-prefix generation in `scripts/contextual-prefix.py`. Verified by full-repo sweep that `cache_control` and the Anthropic API surface exist nowhere else (incl. `claude-canvas/`). No change to retrieval output — API payload shape + observability only.
### Changed
- **Cache only above the Haiku floor** (`scripts/contextual-prefix.py`). The page-body `cache_control` marker is now attached only when the body clears the Haiku 4.5 minimum cacheable size (`HAIKU_CACHE_MIN_CHARS = 16384`, ~4096 tokens × 4 chars/token). Below the floor the Anthropic API silently ignores the marker, so the prior unconditional marker was a no-op that misled the reader. Extracted as the pure, unit-tested `cache_control_for()`.
- `.claude-plugin/plugin.json` + `marketplace.json` version 1.9.1 → 1.9.2.
### Added
- **Cache telemetry** (`scripts/contextual-prefix.py`). The tier-1 path now logs `cache: wrote=<N> read=<N> tok` from the response `usage` fields — integers only, never page content, preserving the v1.7.1 data-egress posture. Implements the docs' "monitor cache hit rates" guidance and reveals whether the body cache is actually firing given the floor.
- **Sequential-invariant note** at the chunk loop (`process_page`), documenting that cache reads depend on chunk 0's response landing before chunk 1 is sent (Anthropic prompt-caching concurrency rule). Guards against a future parallelization silently zeroing every cache read.
- `tests/test_contextual_prefix.py` — hermetic coverage of the `cache_control_for()` floor decision (below / at / above floor, empty body, floor constant matches the documented Haiku minimum). Wired into `make test` (now 9 suites) + `make test-contextual`.
### Documented
- Tier-1 "prompt-cached" claim now states the ~16 KB Haiku floor in the `contextual-prefix.py` module docstring and the ingest diagrams in `docs/compound-vault-guide.md` and `skills/wiki-retrieve/SKILL.md`, so docs match runtime behavior.
### Fixed
- **Explicit missing or out-of-vault page paths now fail cleanly** (`scripts/contextual-prefix.py`). A single explicit path that does not exist exits 3 (was: silent exit 0, swallowed by the `is_file()` filter in `main()`); a path resolving outside the vault exits 2 with a message (was: a raw `ValueError` traceback from `relative_to()`). `--all` runs are unaffected.
- Removed the dead `EXIT_NO_ADDRESS` (exit 5) constant and its docstring entry — it was defined and documented but never raised. Renamed the shadowed `prefix` progress-label variable in `process_page` to `progress`.
### Verification
- `make test`: 9 hermetic suites green; the contextual suite now mocks the API payload to assert `cache_control` attaches only above the floor and the model reply is truncated to one line. No regressions.
- Explicit-path exit codes confirmed by run: missing in-vault path → 3, out-of-vault path → 2, valid page → 0, `--all` unaffected.
- `python3 scripts/contextual-prefix.py wiki/getting-started.md --peek`: tier selection unchanged (synthetic without `--allow-egress`).
- Live tier-1 telemetry leg (sends page bodies off-machine) requires explicit `--allow-egress` and is left to operator verification per the repo's consent design.
## [1.9.1] - 2026-05-18 (v1.9.0 audit hardening)
Patch release closing **6 of 6 remaining HIGH/MEDIUM** findings from the v1.9.0 pre-public-promotion audit ([`docs/audits/v1.9.0-pre-public-promotion-audit-2026-05-18.md`](docs/audits/v1.9.0-pre-public-promotion-audit-2026-05-18.md)) plus 3 LOW hardening items. Composite score moves from 91.6 to ~94 raw average. Public-promotion ship verdict remains GREEN.
### Fixed (defensive hardening)
- **H4 — stale-lock reaper wiring** (`hooks/hooks.json`). New SessionStart command runs `bash scripts/wiki-lock.sh clear-stale --max-age 3600` at every session resume/startup. Locks orphaned by a crashed batch ingest get reaped automatically on the next session, not just on operator demand.
- **S2 — opt-out gate for PostToolUse auto-commit** (`hooks/hooks.json`). Hook now exits early if `.vault-meta/auto-commit.disabled` exists. Default behavior unchanged for existing users; per-vault opt-out is one `touch` away. Useful for shared repos, CI runs, or any scenario where the operator wants to commit manually.
- **Data M3 — symlink canonicalization** (`scripts/wiki-lock.sh:110-142`). `validate_path()` previously rejected literal `..` segments but did not canonicalize symlinks. A symlink inside `wiki/` resolving outside `VAULT_ROOT` could escape. Now resolves via `python3 os.path.realpath` and rejects any path whose canonical form is outside `commonpath(VAULT_ROOT, target)`. Cross-platform (GNU coreutils + macOS BSD); no realpath flag dependency.
- **Data M4 — `.vault-meta/locks/.gitkeep`** + gitignore pattern change. `.vault-meta/locks/*` (not the dir itself) is now ignored; `.gitkeep` is whitelisted so the directory ships on fresh clone. Runtime behavior unchanged (`ensure_dirs()` always created it lazily); this just removes the first-acquire side-effect on directory presence.
- **Data M1 — rerank.py warning routes to hook.log** (`scripts/rerank.py:158-176`). When the embed-cache lock is unavailable after 3 tries, the WARN line now also appends to `.vault-meta/hook.log` with a timestamp, so users see the event via `wiki lint` or by tailing the log. stderr-only was invisible to most callers.
- **S4 — ollama-localhost assert** (`bin/setup-retrieve.sh:97-117`). If `OLLAMA_URL` env var points off-localhost, refuse to probe unless `--allow-remote-ollama` is passed. Mirrors the existing `scripts/tiling-check.py:351` gate. Closes a defense-in-depth gap where a malicious env var could redirect probes to an attacker-controlled endpoint.
### Documented
- **H2 + S3 — multi-tenant threat model** (`SECURITY.md`). New "Threat model: single-tenant vault" section documents three intentional design choices (cross-process lock release, auto-commit hook scope, filesystem-permission trust boundary) and the mitigations for shared-host deployments. Closes the documentation gap the audit flagged: the design choices are correct for single-tenant, but operators in shared-host scenarios deserve to know what changes for them.
### Changed
- `.claude-plugin/plugin.json` + `marketplace.json` version 1.9.0 → 1.9.1.
### Deferred to v1.9.2 (not in this release)
- **Data M2 — embed-cache + chunk-orphan GC**: new `--gc` subcommand for `bm25-index.py` + `contextual-prefix.py` that prunes entries whose backing pages no longer exist. Requires hermetic tests covering edge cases; scoped for a dedicated release.
- **W1 — wiki/meta/ release-session note relocation**: 12 files with incoming wikilinks need a coordinated graph update. Bundled with References M1+M2 (17 dead wikilink targets) for one-pass wiki cleanup.
- **Security S1 — Excalidraw checksum pin**: requires upstream release hash verification + maintenance burden for future releases. Tracked separately.
- **GROW note from v1.9.0 audit — 7th always-check cut in `agents/verifier.md`**: cross-file string consistency check (catches the class of bug where a single-file fix should have been a multi-file cascade, like the 548d294 + F1-F5 sequence).
### Verification
- `make test`: 8 hermetic suites green (~1234 assertions). No regressions.
- Live symlink-escape test on `wiki-lock.sh validate_path`: `ln -s /tmp/foo ./escape && bash scripts/wiki-lock.sh acquire escape/x.md` correctly rejects with "path resolves outside vault via symlink".
- Both plugin manifests parse as JSON.
- Pre-push verifier agent dispatch on staged diff: SHIP, 0 BLOCKER, 0 HIGH.
## [1.9.0] - 2026-05-18 (10-principle thinking framework)
Minor release adding the **10-principle thinking framework** as a first-class layer of the plugin. The framework (OBSERVE-OBSERVE-LISTEN-THINK-CONNECT-CONNECT-FEEL-ACCEPT-CREATE-GROW) is integrated at three levels: as the new `/think` skill, as an appendix on every existing SKILL.md, and as the methodology spine for the v1.8.0 pre-push audit (which used it as its phase structure). Skill count: 14 → **15**.
### Added
- **`skills/think/SKILL.md`** — new skill #15. Canonical source for the 10-principle thinking loop. Walks Claude through external observation, metacognition (the often-skipped one), active listening, first-principles analysis (six-cut kernel lives here), lateral connection, system orchestration, intuition, intellectual humility (anti-sycophancy enforcement), generative output, and iterative growth. Triggers on "think this through", "10-principle review", "/think", "OBSERVE LISTEN THINK", "deep think", "systematic thinking", "structured reasoning". Allowed tools: `Read, Grep, Glob, Bash` (read-only; loads structure and discipline, not mutation). ~250 lines covering the 10 principles with one-paragraph definitions, when-to-invoke guidance, stage-by-stage prompts (5 questions per stage), anti-patterns (the common skips), and composition notes with `/best-practices`, `/save`, `/wiki-lint`, `agents/verifier.md`, and `/autoresearch`.
### Changed
- **All 14 existing SKILL.md files** — each receives a unique "## How to think (10-principle mapping)" appendix at the end. Per-skill 10-row table mapping each principle to that skill's specific work. Examples: wiki-mode's OBSERVE-internal is "audit the assumption that mode=generic is the default"; autoresearch's OBSERVE-internal is "am I steering the search toward what I already expect to find? confirmation bias kills research"; wiki-lint's FEEL is "a lint report should empower, not shame". Each appendix is non-trivial and skill-specific (not a template stub), satisfying the plan's verification rule #12.
- **`.claude-plugin/plugin.json` + `marketplace.json`** — version 1.8.2 → 1.9.0. Description unchanged (the framework is additive to the v1.8.0 + v1.8.2 surface).
### Repo hygiene (first-public-release prep)
- **`CONTRIBUTING.md`** (NEW) — workflow, six-cut self-review checklist, commit conventions, test requirements.
- **`CODE_OF_CONDUCT.md`** (NEW) — adopts Contributor Covenant v2.1 by reference.
- **`SECURITY.md`** (NEW) — private disclosure policy, response SLA, scope, credit policy.
- **`.github/ISSUE_TEMPLATE/bug_report.md`** (NEW) — reproduction + environment + skill-affected fields.
- **`.github/ISSUE_TEMPLATE/feature_request.md`** (NEW) — scope + compatibility + testing fields.
- **`.github/pull_request_template.md`** (NEW) — six-cut self-review + test results + verifier verdict + CHANGELOG reminder.
- **`.github/workflows/test.yml`** (NEW) — CI runs `make test` on push/PR + validates SKILL.md frontmatter + agents `tools:` declaration + plugin manifest JSON validity.
- **Manifest + doc URL updates** — `plugin.json`, `marketplace.json`, and 18 other files updated to reference the canonical repository URL.
### Why this release
Per the v1.8.0 pre-push audit's GROW notes (`docs/audits/v1.8.0-pre-push-audit-2026-05-18.md` §10), the 10-principle framework proved its value as the AUDIT's mental spine — OBSERVE-internal forced explicit bias documentation; GROW forced a feedback-loop section. Shipping it as a first-class skill (and as appendices on all existing skills) makes the discipline available to every future invocation, not just to one-off audits. This is the GROW step of the audit itself, embodied in code.
### Compass axis status after v1.9.0
| Axis | v1.8.0 | v1.9.0 |
|---|---|---|
| Compounding wiki primitive | #1 | #1 |
| Multi-writer safety | #1 | #1 |
| Retrieval architecture (free tier) | #1 | #1 |
| License / openness | #1 | #1 |
| Methodology support | #1 | #1 (deepened by framework integration) |
| Derivative outputs | NO | NO (v2.0 scope) |
| GUI / install ergonomics | NO | NO (v2.5+ scope) |
5 of 7 axes #1 (unchanged count, but methodology axis deepens — claude-obsidian is now the only Claude+Obsidian plugin shipping methodology modes AND a first-class thinking-loop framework AND per-skill thinking guidance).
### Migration notes
- v1.8.x vaults: no action needed. All existing skills work identically; the "How to think" appendix is additive guidance, not behavioral change.
- `/think` is invocable from any project that has this plugin installed; it does not require a vault.
- The framework can be invoked explicitly (`/think <problem>`) or applied implicitly when an existing skill's appendix references it.
### Composition
- `/think` + `/save` = the canonical compounding loop. Apply the 10 principles to a problem; when done, save the insights worth not re-deriving.
- `/think` + `/best-practices` = engineering discipline at the THINK stage of the framework. The six-cut kernel IS the inside of stage 4.
- `/think` + `agents/verifier.md` = an OBSERVE-internal substitute for solo work — fresh-context reviewer that catches biases the chair missed.
## [1.8.2] - 2026-05-18 (pre-push audit closure)
Patch release closing **all 4 HIGH findings + 1 leaked BLOCKER-class hardening** from the v1.8.0 pre-push audit. Audit: [`docs/audits/v1.8.0-pre-push-audit-2026-05-18.md`](docs/audits/v1.8.0-pre-push-audit-2026-05-18.md). Per the audit's strict push gate (any BLOCKER halts), v1.8.2 takes the release from YELLOW (0 BLOCKER / 4 HIGH) to GREEN (0 BLOCKER / 0 HIGH).
### Fixed
- **H1 — `scripts/detect-transport.sh`: implement `manual_override`.** The documented escape hatch for MCP-only users (`"manual_override": true` in `transport.json`) was documented at `wiki/references/transport-fallback.md` but never honored by the script. v1.8.2 parses the existing snapshot BEFORE auto-detection; when `manual_override: true`, the user's `preferred` and `fallback_chain` are preserved across normal cycles AND `--force` refreshes. Auto-detection still runs to refresh the `available.cli.*` informational fields. Field round-trips through the JSON schema (new `"manual_override": <bool>` in every snapshot). Verified by smoke test: a pinned `"preferred": "mcp-obsidian"` survived a `--force` refresh.
- **H2 — `agents/wiki-ingest.md`: add `Bash` to tools + add `## Mode awareness (v1.8+)` section.** The parallel batch-ingest sub-agent was missing `Bash` in its `tools:` frontmatter despite mandating `bash scripts/wiki-lock.sh acquire/release` in its body — this defeated the v1.7 multi-writer safety guarantee. Sub-agent was also missing v1.8 mode-routing awareness, so batch-ingest in LYT/PARA/Zettelkasten vaults filed to v1.7 generic paths. Both gaps closed.
- **H3 — `skills/autoresearch/SKILL.md`: new `## Web egress hygiene (v1.8.2+)` section.** Four sub-policies: (1) URL validation (reject `file://`, `javascript:`, RFC1918), (2) content sanitization before write (strip `<script>`/`<iframe>`, escape `[[/]]` injections, reject embedded frontmatter delimiters, 50KB truncation), (3) per-loop cost expectation (~45 WebFetch calls per run), (4) failure mode (log to `wiki/log.md`, never silently swallow). The router's `safe_name()` is the FILENAME guard; this is the BODY-content guard.
- **H4 — `skills/save/SKILL.md`: prepend `Step 0: Decide the destination root`.** The skill body assumed project-local `wiki/` filing while the global `~/.claude/CLAUDE.md` `/save` rule mandates personal-vault filing for cross-project saves. Step 0 makes the routing decision explicit with three rules in order: user-explicit override → project/global CLAUDE.md `/save` override → project-local `wiki/` default. Path sanitization still applies regardless of destination root. Workflow step 5 now requires a collision check (ASK before overwrite).
- **wiki/references/transport-fallback.md:** §Manual override now describes the actual v1.8.2 behavior (preserves `preferred`+`fallback_chain` while still refreshing `available.cli.*`; field round-trips through snapshot).
### Changed
- **`.claude-plugin/plugin.json` + `marketplace.json`:** version 1.8.0 → 1.8.2.
- **`docs/audits/v1.8.0-pre-push-audit-2026-05-18.md`** (NEW): full pre-push audit report. 14 per-skill scores (average 84.6/100), per-tier finding ledger, v1.8.2 fix replay, hook safety, manifest accuracy, push-gate decision tree. Audit methodology used the 10-principle thinking spine (OBSERVE-OBSERVE-LISTEN-THINK-CONNECT-CONNECT-FEEL-ACCEPT-CREATE-GROW) as audit phases.
### Verification
- All 8 hermetic test suites green (~1234 assertions): allocate-address, tiling-check, boundary-score, bm25-index, retrieve, wiki-lock, concurrent-write, wiki-mode.
- v1.8.2 manual_override smoke test: pinned `preferred="mcp-obsidian"` survived `--force` refresh.
- All path-traversal attack vectors against `route_path()` confirmed sanitized inside vault root (6 dedicated assertions).
- mkstemp atomic write yields 0600 perms (verified via `stat`).
- `--mode` preview is non-mutating (verified via mtime).
### Known issues at v1.8.2 (deferred to v1.9 or later)
The pre-push audit also surfaced 14 MEDIUM and 45 LOW findings. None block release. Triage in audit §12. Highlights:
- `wiki-cli` mcp-obsidian + mcpvault tiers documented as fallback positions 2/3 but unreachable from auto-detection (deferred — manual_override is the workaround until MCP auto-detect ships in v1.7.x patch).
- No `tests/test_detect_transport.sh` yet for v1.7+ transport script (planned v1.8.3).
- 7 skills declare incomplete `allowed-tools` lists (missing `Bash` despite shelling out) — works in practice (harness default-allows), but convention violation (planned v1.8.3).
- `tests/__init__.py` missing → `python3 -m unittest tests.X` form fails (direct invocation works) (planned v1.8.3).
- Various doc/reality drift around the v1.8 ID format change (14-digit → 20-digit), v1.8 `--mode` flag not yet referenced in consumer docs (deferred LOW polish PR).
## [1.8.0] - 2026-05-17 (methodology modes — closes compass priority gap 5)
Minor release closing the **5th and final priority gap** from the May 2026 compass artifact: methodology support. Adds the **`wiki-mode`** skill with first-class support for four organizational styles (LYT / PARA / Zettelkasten / Generic). After this release, claude-obsidian is **#1 on 5 of 7 axes per compass framework** — up from 4/7 in v1.7. Full guide: [`docs/methodology-modes-guide.md`](docs/methodology-modes-guide.md).
### Added
- **`skills/wiki-mode/SKILL.md`** — new skill (skill #14). Reads `.vault-meta/mode.json`; defaults to `generic` (v1.7 behavior) when absent. Triggers on "set vault mode", "switch to PARA", "use LYT", "zettelkasten setup", etc.
- **`scripts/wiki-mode.py`** — pure-stdlib router + config helper. Subcommands: `get` (current mode), `config` (full JSON), `route <type> <name>` (suggested path), `set <mode>` (write mode.json), `id` (mint Zettel timestamp ID), `templates` (list per-mode templates).
- **`bin/setup-mode.sh`** — interactive setup with `--mode <name>` non-interactive flag. Idempotent; safe to re-run to switch modes. Optionally seeds template folders for the chosen mode.
- **6 per-mode templates** under `skills/wiki-mode/templates/`:
- `lyt/moc-template.md`, `lyt/atomic-template.md`
- `para/project-template.md`, `para/area-template.md`, `para/resource-template.md`
- `zettel/atomic-template.md`
- **`tests/test_wiki_mode.py`** — hermetic test suite (15 assertions covering load/save round-trip, all 4 modes' routing, slugify Unicode handling, Zettel ID format, corrupted-config fallback, CLI subprocess paths). `make test` is now **8 suites**.
- **`docs/methodology-modes-guide.md`** — narrative guide; when-to-use-which decision tree per mode; full schema documentation; migration guidance.
### Changed
- **`skills/wiki-ingest/SKILL.md`** — new "## Mode awareness (v1.8+)" section. Skill now consults `wiki-mode.py route` before filing new source/entity/concept pages. mode=generic preserves v1.7 behavior byte-for-byte.
- **`skills/save/SKILL.md`** — new "## Mode awareness (v1.8+)" section. Session notes now route per active mode (with explicit note that the global `~/Documents/Obsidian Vault/sessions/` rule still applies to cross-project saves).
- **`skills/autoresearch/SKILL.md`** — new "## Mode awareness (v1.8+)" section. Research synthesis output routes per active mode; every new entity/concept page in the research loop also routes via the router.
- **`Makefile`** — new `test-mode` and `setup-mode` targets; `test` aggregate now runs 8 suites; `clean-test-state` removes `.vault-meta/mode.json` + `.vault-meta/hook.log`.
- **`.gitignore`** — `.vault-meta/mode.json` + `.vault-meta/mode.*.tmp` added. Host-specific runtime config by default; `git add -f` to commit if the user wants the mode choice to follow the repo.
- **`CLAUDE.md`** — new "## Methodology Modes (v1.8+)" section + skill table row + plugin-name header reference.
- **`.claude-plugin/plugin.json` + `marketplace.json`** — version 1.7.2 → 1.8.0; descriptions refreshed to mention methodology modes and "5 of 5 priority gaps closed."
### Compass axis status after v1.8.0
| Axis (compass §1 + audit §9) | v1.7.2 | v1.8.0 |
|---|---|---|
| Compounding wiki primitive | #1 | #1 |
| Multi-writer safety | #1 | #1 |
| Retrieval architecture (free tier) | #1 | #1 |
| License / openness | #1 | #1 |
| **Methodology support** | TIE | **#1 ← v1.8.0** |
| Derivative outputs | NO | NO (v2.0 scope) |
| GUI / install ergonomics | NO | NO (v2.5+ scope) |
**5 of 7 axes #1.** Remaining 2 axes require multi-release effort.
### Honest scope acknowledgment
- "Best ever obsidian skill per the priority research" = the 5 priority gaps closed. **v1.8.0 reaches this milestone.**
- "Best ever in the market" requires **v2.0** (derive — audio/quiz/study) + **v2.5+** (Community Plugin GUI fork). These are weeks of work per release; v1.8.0 is the foundation, not the substitute.
- The v1.7.0 audit's 24 findings (1 BLOCKER + 6 HIGH + 10 MEDIUM + 7 LOW) are fully CLOSED-or-DEFERRED as of v1.7.2; v1.8.0 inherits a clean audit ledger.
### Migration notes
- v1.7.x vaults: no action needed. `wiki-mode` defaults to `generic` when `.vault-meta/mode.json` is absent, which is identical to v1.7 behavior. The mode-awareness sections in wiki-ingest/save/autoresearch are no-ops in generic mode.
- To adopt a non-default mode: `bash bin/setup-mode.sh` (or `bash bin/setup-mode.sh --mode <name>`). Interactive prompt picks one of LYT/PARA/Zettelkasten/Generic; optionally seeds template folders.
- Switching modes does NOT auto-migrate existing files. Manual migration via file manager or `git mv`.
## [1.7.2] - 2026-05-17 (SSS+ convergence — closes every audit finding)
Patch release closing **every remaining MEDIUM (M1-M10) and LOW (L1-L7) finding** from the v1.7.0 audit. Combined with v1.7.1 (which closed the 1 BLOCKER + 6 HIGH), this means the v1.7.0 audit's full 24-finding ledger is now CLOSED or formally DEFERRED-with-rationale. Plan: [`docs/audits/v1.7.2-sss-plus-plan.md`](docs/audits/v1.7.2-sss-plus-plan.md).
### Added
- **`agents/verifier.md` two new "always check" cuts** (`83d18ea`): #5 Git hygiene (any new written path NOT in .gitignore → HIGH; would have caught the v1.7.1 `.vault-meta/hook.log` self-pollution bug mechanically); #6 Additive-without-pruning (if `git diff --shortstat main..HEAD` shows >+500 LOC with <50 deletions, flag MEDIUM). Verifier learns from what its prior dispatches missed.
- **Unicode multilingual test** (`8c219fb`): `tests/test_bm25_index.py::test_tokenize_unicode_multilingual` covers Cyrillic, CJK, accented Latin, pure-emoji skip, mixed ASCII+non-ASCII.
- **`--explain` + `--no-rerank` test coverage** (`a80ae61`): `tests/test_retrieve.py` now exercises both flags hermetically (test_explain_flag_adds_diagnostics_block + test_no_rerank_flag_strategy_bm25_only). +6 assertions.
- **Newline + carriage-return path rejection tests** (`d0db354`): `tests/test_wiki_lock.sh` +2 assertions for the new validate_path rejections.
- **`[i/total]` progress prefix on contextual-prefix.py per-page logs** (`59cd7c8`): Stage 1 over 47 pages with tier-2 (claude-cli) takes 5+ min; user now sees position, not just opaque per-page lines.
### Changed (defensive-input + correctness fixes)
- **M2 — Unicode-aware BM25 tokenizer** (`8c219fb`): `[A-Za-z][A-Za-z0-9'\-]*` → `\w[\w'\-]*` with `re.UNICODE`. CJK / Cyrillic / Devanagari / accented Latin vaults previously had content silently dropped at index time. Same regex mirrored in `scripts/baseline-v16.py` so v1.6/v1.7 retrieval comparisons stay apples-to-apples for non-ASCII corpora.
- **M3 — `scripts/rerank.py` off-localhost error rewritten** (`d0db354`): from "pass --allow-remote-ollama" to a 3-option breakdown citing the actual host, concrete recovery steps for each option, and the canonical paths.
- **M4 — `scripts/wiki-lock.sh validate_path()` rejects newlines + carriage returns** (`d0db354`): would have silently corrupted the meta-lock line format.
- **M5 — `scripts/retrieve.py import_sibling()` wraps in try/except** (`d0db354`): ImportError / SyntaxError / AttributeError now produce friendly diagnostics with recovery hints (`bash bin/setup-retrieve.sh --check`) instead of bare Python tracebacks. Pre-checks target file existence.
- **M6 — `scripts/contextual-prefix.py` empty-body WARN** (`d0db354`): frontmatter-only pages now produce explicit `WARN: ... has no chunkable body content` instead of silent `chunks=0`.
- **M7 — `scripts/rerank.py save_cache()` non-blocking lock + 3-attempt retry** (`d0db354`): replaces blocking `fcntl.LOCK_EX` (no timeout) with `LOCK_NB` + 100ms retry; falls back to unlocked write with WARN if all 3 attempts fail. Prevents indefinite hang on NFS / FUSE mounts without lock support. The temp+rename pattern provides write atomicity even unlocked.
- **L2 — Stage 1 progress indicator** (`59cd7c8`): per-page log lines now carry `[i/total]` prefix.
- **L6 — `scripts/wiki-lock.sh` header doc** (`59cd7c8`): explicit distinction between `STALE_AFTER_SEC` (per-acquire, default 60s) and `clear-stale --max-age` (admin reaper, default 3600s). Both time-since-acquire but distinct scopes.
- **L7 — `scripts/bm25-index.py` BM25 divide guard** (`59cd7c8`): `avg_dl_safe = avg_dl or 1.0`. Currently unreachable but invariant-by-construction now rather than emergent-from-reachability.
### Removed (kernel: "delete more than you add")
- **L3 — dead `bm25_score()` function** (`eafd449`): 28 lines, never called, self-documented as "placeholder; real score computed in query()". Removed.
- **L4 — `--rebuild` flag stub** on `scripts/bm25-index.py build` (`eafd449`): declared but never read; was reserved for incremental mode not in v1.7. Per kernel: no abstraction without 3 real callers.
- **L5 — `--no-bm25` flag stub** on `scripts/retrieve.py` (`eafd449`): returned `EXIT_USAGE` with "reserved for v1.7.x vector-only mode." Same kernel principle.
### Honest accounting
- **Net LOC delta `main..HEAD` is `+6009 / -30`**, NOT meeting the plan §1 acceptance criterion (`≤+5000 OR ≥-200`). Per plan §4 failure clause: "Do not invent prunes to game the metric." Honest decomposition: ~5500 LOC across new files alone (4 new scripts + 4 new tests + 2 new skills + 1 new agent + 1 new bin + ~2200 LOC docs). The v1.7 line was net-new feature substrate, not a refactor; v1.6 had no equivalent of a retrieval pipeline, lock primitive, transport detector, or contextual prefix generator to delete. **Kernel-application axis ceilings at ~92-95** for the v1.7 line; the deduction is structural to building substrate, not negligence. Documented in `docs/audits/v1.7.0-audit-2026-05-17.md` §10.2.
- **M9 (bounded-slices: 4 skills touched by both §3.2 and §3.4)** is documented as a process note in audit §10.3; not a code-level fix.
- **M11 (synonym category benchmark tied 60%/60%)** persists post-tokenizer-change; v1.7 hybrid neither helps nor hurts on this category. Filed for v1.7.x rerank threshold tuning.
- **M12 (negative-query precision)** was tied at 40%/40% in v1.7.0; post-Unicode-tokenizer it's 40%/20% (+20pp). Empirically closed by the tokenizer change.
- **L1 (§3.1 substrate +17/-5 no deletion)** documented as defensible process note in audit §10.3.
### Benchmark refresh (full 50-query corpus, v1.7.2 measurement)
Run via `python3 scripts/benchmark-runner.py`:
| Category | N | v17 top-1 | v17 top-5 | v16 top-1 | v16 top-5 | Δ top-1 |
|---|---|---|---|---|---|---|
| cross-page | 10 | 20.0% | 80.0% | 30.0% | 40.0% | -10.0pp |
| derived | 25 | 68.0% | 88.0% | 12.0% | 24.0% | +56.0pp |
| negative | 5 | 40.0% | 80.0% | 20.0% | 80.0% | +20.0pp |
| partial-recall | 5 | 60.0% | 100.0% | 20.0% | 60.0% | +40.0pp |
| synonym | 5 | 60.0% | 100.0% | 60.0% | 100.0% | +0.0pp |
| **TOTAL** | **50** | **54.0%** | **88.0%** | **22.0%** | **44.0%** | **+32.0pp** |
**Error reduction: +41.0%** vs the ≥30% ship gate — PASS.
The +32pp/41% slightly beats the v1.7.0 audit's reported +30pp/+39.5%; the Unicode tokenizer change made baseline-v16.py marginally weaker (−2pp on its top-1) which counts as a delta improvement for v1.7. cross-page top-1 regression vs audit (was +0pp, now −10pp) is within benchmark noise on N=10; cross-page top-5 stayed at 80% which is the synthesis-relevant metric.
### Migration notes
- v1.7.1 vaults: no action needed. All v1.7.2 changes are backward-compatible behavior improvements.
- Re-running `bash bin/setup-retrieve.sh` is recommended (rebuilds BM25 index with the new Unicode tokenizer; multilingual content that was silently dropped will now be indexed).
- The v1.7.0 audit's full 24-finding ledger is now CLOSED-or-formally-DEFERRED. v1.7.2 marks the end of the v1.7 line's audit-debt remediation cycle.
## [1.7.1] - 2026-05-17 (audit-driven patch)
Patch release closing the 1 BLOCKER + 6 HIGH findings from the v1.7.0 audit ([`docs/audits/v1.7.0-audit-2026-05-17.md`](docs/audits/v1.7.0-audit-2026-05-17.md)). All v1.7.0 features remain available; the changes are guard-rails and one new agent.
### Fixed
- **BLOCKER B1 — Data egress without consent** (`ca68bb6`). `scripts/contextual-prefix.py` now requires an explicit `--allow-egress` flag (default off) before selecting tier-1 (Anthropic API) or tier-2 (claude CLI subprocess). Without the flag, `pick_prefix_tier()` returns `"synthetic"` regardless of `ANTHROPIC_API_KEY` or `claude` binary presence. `bin/setup-retrieve.sh` adds a y/N consent prompt before any non-synthetic Stage 1 run. `skills/wiki-retrieve/SKILL.md` adds a Data Privacy callout (also closes H6). Mirror of the existing `scripts/tiling-check.py:351` `--allow-remote-ollama` precedent.
- **H1 — Stage 1 failure had no rollback path** (`4837d4f`). `bin/setup-retrieve.sh` now captures Stage 1's exit code, exits 5 on non-zero, and prints a 3-option recovery hint (incremental resume, full wipe, single-page re-process). Stage 2 only runs after Stage 1 success.
- **H2 — `make clean-test-state` didn't remove v1.7 artifacts** (`7e1f187`). Extended the target to remove `.vault-meta/chunks/`, `.vault-meta/bm25/`, `.vault-meta/locks/`, `.vault-meta/transport.json`, `.vault-meta/.wiki-lock.meta`, and the related `.tmp` files. The Makefile target now matches the v1.7 `.gitignore` set.
- **H3 — PostToolUse hook swallowed lock-check errors** (`7120970`). Restructured `hooks/hooks.json` to capture the wiki-lock script's exit code directly (not via a pipeline), defer the auto-commit on any non-zero rc, and only run `git add` after both the rc check and the non-empty-list check pass.
- **H4 — No verifier-agent pass at workstream gates** (`3ea443f`). Added `agents/verifier.md` — a read-only (`Read`/`Grep`/`Glob`/`Bash` only; no `Write`/`Edit`) pre-commit specialist that reads the staged diff, applies the /best-practices six-cut + agent kernel, and returns findings in four tiers (BLOCKER/HIGH/MEDIUM/LOW). CLAUDE.md "Pre-commit verifier (v1.7.1+)" section references it as the recommended pre-commit step.
- **H5 — `detect-transport.sh` JSON escaping was shell-only** (`722ac97`). Added a `json_escape()` helper that pipes through `python3 -c json.dumps`, applied to `CLI_VERSION` (both `obsidian-cli` and `obsidian`-binary paths). The heredoc now emits `${CLI_VERSION}` without surrounding quotes since the helper produces a pre-quoted JSON string. Defense in depth against pathological upstream version output (backslashes, tabs, newlines, control chars).
- **H6 — `skills/wiki-retrieve/SKILL.md` had no Data Privacy section** (bundled with B1 in `ca68bb6`). New section at the top of the skill body documents the two-layer egress guard (`--allow-egress` flag + setup-retrieve prompt) and points back to the `tiling-check.py` precedent.
### Added
- `agents/verifier.md` — pre-commit specialist; see H4 above.
- `scripts/baseline-v16.py` + `scripts/benchmark-runner.py` — audit instrumentation that ran the 50-query retrieval benchmark documented in `wiki/meta/retrieval-benchmark-v1.7.md`. Result: v1.7 top-1 54.0% vs v1.6 baseline 24.0% (+30pp); error reduction +39.5% vs the ≥30% gate. Future audits can re-run with `python3 scripts/benchmark-runner.py`.
- `docs/audits/v1.7.0-audit-2026-05-17.md` (481 lines) — the full audit report.
- `docs/audits/v1.7.1-fixes-plan.md` — the sequenced 6-commit roadmap this release executes.
### Changed
- Versions bumped to 1.7.1 in `.claude-plugin/plugin.json` and `.claude-plugin/marketplace.json` (description fields refreshed to mention the verifier agent and the egress-consent guard).
- `CLAUDE.md` "Pre-commit verifier (v1.7.1+)" section added; "Concurrency (v1.7+)" section retained verbatim.
### Polish (post-fix self-audit refinements)
After the 7 v1.7.1 commits landed, a re-pass with `agents/verifier.md` against the slice surfaced 2 MEDIUM + 3 LOW polish items. All closed in one follow-up commit:
- `scripts/detect-transport.sh` — split `CLI_VERSION_RAW` (human log line) from `CLI_VERSION` (pre-quoted JSON for the heredoc). The JSON-escape fix from H5 made the log line `CLI: obsidian-cli ("1.12.0")` carry visible quotes; the split keeps both paths clean. **Also**: `CLI_VERSION_RAW=""` initialized in the top-of-script init block alongside `CLI_PRESENT`, `CLI_BINARY`, `CLI_VERSION` (defense in depth under `set -euo pipefail`; closes a latent unbound-variable risk that worked today only by bash short-circuit semantics).
- `agents/verifier.md` — `tools:` field kept as CSV (`Read, Grep, Glob, Bash`) to match in-repo precedent (`wiki-ingest.md`, `wiki-lint.md`). Both CSV and YAML list are accepted forms across `~/.claude/agents/` (audit-* use CSV, blog-* and challenge-auditor-* use YAML list), but the three local repo agents are CSV, so consistency-with-siblings is the deciding factor. The polish commit initially converted to YAML list per a prior verifier recommendation that didn't cross-check sibling files; reverted in the follow-up after deeper chair probe.
- `bin/setup-retrieve.sh` — refreshed the header docstring (lines 13-26) to mention `--allow-egress` and the consent gate. Inline comments at line 121 were already correct; the file-top doc was the stale one.
- `scripts/contextual-prefix.py` — docstring on `generate_prefix()` explaining the deliberate asymmetric fallback (api→cli→synthetic, but cli→synthetic only — climbing from cli to api would silently spend money the user did not authorize).
- `hooks/hooks.json` — breadcrumb log to `.vault-meta/hook.log` on the rare non-zero `LOCK_RC` defer path. Verified with concurrency (10 parallel hook fires → 10 atomic lines, no interleaving; line length < `PIPE_BUF`), no format-string injection (printf uses literal format with %s placeholders), filesystem-failure edge cases preserve `exit 0` (defer behavior intact). **`.vault-meta/hook.log`** added to `.gitignore` so the breadcrumb file is never auto-staged by the same PostToolUse hook (closes a self-pollution loop that would have surfaced on the first non-zero `LOCK_RC` event).
### Migration notes
- v1.6 vaults: no action needed. The new components are opt-in or read-only.
- v1.7.0 adopters who provisioned `bin/setup-retrieve.sh` and had `ANTHROPIC_API_KEY` set: the next `bin/setup-retrieve.sh` run will prompt for consent before proceeding with the non-synthetic tier. Decline to keep all data on-machine (tier-3 synthetic), accept to preserve the prior behavior. Existing chunks/ data is unaffected either way.
- Test suite: `make test` continues to run 7 hermetic suites (~1162 assertions). Zero ollama, zero network dependency.
## [1.7.0] - 2026-05-17 (Compound Vault refoundation)
The v1.7 line, codenamed **Compound Vault**, refoundations the plugin around four pillars from the May 2026 gap analysis: substrate alignment with `kepano/obsidian-skills`, Obsidian-CLI-native transport, contextual + hybrid retrieval, and safe multi-writer ingest. v1.6 vaults that never install the new opt-in components see no behavior change. Full design rationale in `docs/compound-vault-guide.md`.
### Added
- **§3.2 Default transport** — `skills/wiki-cli/SKILL.md` (recipe reference for Obsidian CLI), `scripts/detect-transport.sh` (writes `.vault-meta/transport.json` snapshot; auto-stale at 7d), `wiki/references/transport-fallback.md` (canonical decision tree). 5 transport-aware skills (wiki-ingest, wiki-query, save, autoresearch, wiki-lint) gained "## Transport (v1.7+)" sections.
- **§3.3 Hybrid retrieval pipeline (wiki-retrieve, opt-in)** — implements Anthropic's Sept 2024 Contextual Retrieval pattern as agent-skill plumbing. 4 new scripts: `scripts/contextual-prefix.py` (3-tier auto: Anthropic API → claude CLI subprocess → synthetic), `scripts/bm25-index.py` (Okapi BM25, k1=1.5 b=0.75, pure stdlib, flock-guarded), `scripts/rerank.py` (cosine on nomic-embed-text via ollama, embed-cache), `scripts/retrieve.py` (orchestrator: BM25 top-20 → rerank top-5 → page dedupe). `bin/setup-retrieve.sh` opt-in bootstrap. `skills/wiki-retrieve/SKILL.md` documents the architecture and cost ceiling (~$12/1000 docs per Anthropic). Wired into `skills/wiki-query/SKILL.md` via "## Retrieval (v1.7+)" section with graceful exit-10 fallback to the v1.6 hot→index→drill read order.
- **§3.4 Multi-writer safety (wiki-lock, core)** — `scripts/wiki-lock.sh` per-file advisory locking. Age-based staleness (default `STALE_AFTER_SEC=60`), cross-process release allowed by design. 4 skills (wiki-ingest, wiki-fold, save, autoresearch) gained "## Concurrency (v1.7+)" sections with concrete acquire/release recipes. The latent corruption bug from v1.6 — documented but unenforced in `skills/wiki-ingest/SKILL.md:259-264` — is now closed.
- **New skills (2)**: `wiki-cli` (§3.2) and `wiki-retrieve` (§3.3). Total skill count is now 13.
- **New scripts (6)**: `detect-transport.sh`, `contextual-prefix.py`, `bm25-index.py`, `rerank.py`, `retrieve.py`, `wiki-lock.sh`.
- **New tests (4)**: `tests/test_bm25_index.py` (~30 hermetic assertions including BM25 monotonicity and IDF positivity), `tests/test_retrieve.py` (22 hermetic assertions including end-to-end subprocess test), `tests/test_wiki_lock.sh` (14 hermetic assertions including age-based stale reap), `tests/test_concurrent_write.sh` (6 hermetic assertions; the critical multi-writer correctness gate — 10 parallel workers, no losses, no garbled lines). `make test` now runs 7 suites with zero network and zero ollama dependency.
- **New docs**: `docs/compound-vault-guide.md` (omnibus v1.7 guide), `wiki/references/transport-fallback.md` (transport decision tree).
- **Makefile targets**: `test-bm25`, `test-retrieve`, `test-lock`, `test-concurrent`, `setup-retrieve`.
### Changed
- **§3.1 Substrate hard-prefer on `kepano/obsidian-skills`** — `skills/obsidian-markdown/SKILL.md`, `skills/obsidian-bases/SKILL.md`, and `skills/canvas/SKILL.md` upgraded from soft-defer ("if kepano installed, prefer it") to hard-prefer ("this is a fallback; prefer kepano"). Architectural behavior unchanged; signal sharpened. `skills/defuddle/SKILL.md` documented as canonical (kepano does not ship a defuddle skill). `.claude-plugin/marketplace.json` declares `recommendedCompanions: [kepano/obsidian-skills]` with install hint.
- **`hooks/hooks.json` PostToolUse** — added a lock-in-flight check before `git add`. When `bash scripts/wiki-lock.sh list` returns non-zero count, the auto-commit defers. Prevents torn commits during multi-agent ingest. Falls through gracefully if `wiki-lock.sh` is absent.
- **`agents/wiki-ingest.md`** — rewrote the "Sub-agents MUST NOT" section. The prohibition on calling `allocate-address.sh` from sub-agents is preserved (counter monotonicity). A NEW rule is added: sub-agents MAY now write pages, but MUST acquire locks first.
- **Versions** synced to 1.7.0 across `plugin.json` and `marketplace.json`.
### Migration notes
- v1.6 vaults need no action. The new components are opt-in (`bash bin/setup-retrieve.sh` for hybrid retrieval) or universally beneficial (wiki-lock is core; no setup needed). The plugin remains MIT-licensed; no paid tier introduced.
- To install the recommended companion: `claude plugin marketplace add kepano/obsidian-skills`. Existing local fallbacks remain functional without it.
- Estimated upgrade time: 5 minutes (substrate auto-detected; transport auto-detected on first session; retrieval requires explicit `bash bin/setup-retrieve.sh`).
### Out of scope for v1.7 (deferred to v1.8+)
- Methodology modes (LYT / PARA / Zettelkasten / Generic via `wiki-mode` skill) — planned for v1.8.
- NotebookLM-class derivative outputs (audio, quiz, flashcards, study guide via `wiki-derive`) — planned for v1.9 or v2.0.
- Multimodal ingest adapters (YouTube, PDF, EPUB, image OCR via `wiki-ingest-multimodal`) — planned for v1.9.
- Periodic review artifacts (`wiki-review`) — planned for v1.8.
## [1.6.0] - 2026-04-24
### Added (DragonScale Mechanism 4, opt-in)
- **Boundary-first autoresearch**: `scripts/boundary-score.py` computes `(out_degree - in_degree) * recency_weight` across the wikilink graph and emits top-K frontier pages. `/autoresearch` invoked without a topic now offers the top-5 frontier pages as research candidates when the vault has adopted DragonScale.
- `tests/test_boundary_score.py` — 35 unit tests covering frontmatter parsing, recency weight, wikilink extraction (with code-block guard), graph construction, scoring, CLI interface.
- `make test-boundary` target + integration into `make test`.
### Changed
- `skills/autoresearch/SKILL.md` — new Topic Selection section with three paths: explicit (A), boundary-first (B, opt-in), user-ask (C, default without DragonScale).
- `commands/autoresearch.md` — no-topic usage documented for both modes.
- `wiki/concepts/DragonScale Memory.md` — Mechanism 4 flipped from NOT IMPLEMENTED to shipped; exact scoring formula and "what is NOT included" callout added. Version bumped to v0.4.
- Version synced to 1.6.0 across plugin.json and marketplace.json.
## [1.5.1] - 2026-04-24 (Phase 3.6 hardening)
### Fixed
- `scripts/tiling-check.py`: `--report PATH` now resolved against VAULT_ROOT and rejected if it escapes (security: prevents hostile or accidental writes outside the vault).
- `.vault-meta/legacy-pages.txt`: rollout baseline corrected from 2026-04-24 to 2026-04-23 (matches earliest addressed page in the seed vault).
- `AGENTS.md`: wiki-fold listed in the skills table; stale claim that "all skills use only name/description" narrowed to newer skills (older skills still carry allowed-tools for Claude Code compatibility).
- `skills/wiki-ingest/SKILL.md`: resolves the internal contradiction between "immutable .raw/" and "maintain .raw/.manifest.json" — user-dropped source documents remain immutable; only the manifest is wiki-ingest-maintained.
- `docs/install-guide.md`: version 1.2.0 -> 1.5.0 with a DragonScale optional-install callout.
## [1.5.0] - 2026-04-24
### Added (DragonScale Memory extension, opt-in)
- **Mechanism 1 — Fold operator** (`skills/wiki-fold/`): extractive, structurally-idempotent rollups of `wiki/log.md` entries into per-batch meta-pages under `wiki/folds/`. Dry-run via stdout by default (does not trigger PostToolUse auto-commit hook); commit mode explicit.
- **Mechanism 2 — Deterministic page addresses** (opt-in): `scripts/allocate-address.sh` flock-guarded atomic allocator; new `address: c-NNNNNN` frontmatter convention; re-ingest idempotency via `.raw/.manifest.json address_map`. `wiki-ingest` and `wiki-lint` skills feature-detect DragonScale setup.
- **Mechanism 3 — Semantic tiling lint** (opt-in): `scripts/tiling-check.py` uses local `nomic-embed-text` via ollama to flag candidate duplicate pages by cosine similarity. Banded thresholds (error/review/pass) documented as conservative seeds with manual calibration procedure.
- `wiki/concepts/DragonScale Memory.md` — full design spec (v0.3) with four mechanisms, scope boundary, and primary-source citations.
- `bin/setup-dragonscale.sh` — idempotent installer that provisions `.vault-meta/` counter, thresholds, and legacy-pages manifest.
- `tests/` — shell + python test suite for the allocator and tiling-check. Run via `make test`.
- `Makefile` — developer targets (`test`, `setup-dragonscale`, `clean-test-state`).
### Changed
- `hooks/hooks.json` PostToolUse now stages `.vault-meta/` in addition to `wiki/` and `.raw/` so DragonScale runtime state is captured by the auto-commit hook.
- `skills/wiki-ingest/SKILL.md` and `skills/wiki-lint/SKILL.md` gained opt-in DragonScale sections behind feature-detection guards; original behavior unchanged for vaults that have not run `setup-dragonscale.sh`.
- `agents/wiki-ingest.md` explicitly forbids parallel sub-agents from calling the allocator (single-writer rule for address assignment).
- `agents/wiki-lint.md` extended to describe Address Validation and Semantic Tiling checks.
- Stale `allowed-tools` frontmatter removed from `wiki-ingest` and `wiki-lint` SKILL.md (kepano convention: only `name` and `description`).
- Version strings synced across `.claude-plugin/plugin.json`, `.claude-plugin/marketplace.json`, and documentation.
### Security
- `scripts/tiling-check.py` locks `OLLAMA_URL` to localhost by default. Remote endpoints require `--allow-remote-ollama`. Symlinks and vault-root escapes are rejected before any read.
### Not in this release
- **Mechanism 4 — Boundary-first autoresearch**: documented in the spec as a future proposal; no code shipped. `skills/autoresearch/SKILL.md` unchanged.
## [1.4.3] - prior
Previous state. See git log for details.
CITATION.cff
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cff-version: 1.2.0
title: claude-obsidian
message: >-
If you use this software, please cite it using the metadata from this file.
type: software
authors:
- alias: AgriciDaniel
repository-code: 'https://github.com/AgriciDaniel/claude-obsidian'
url: 'https://github.com/AgriciDaniel/claude-obsidian'
license: MIT
version: 1.9.2
date-released: '2026-05-28'
keywords:
- obsidian
- claude-code
- knowledge-management
- second-brain
- pkm
- llm-wiki
- rag
CLAUDE.md
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# claude-obsidian — Claude + Obsidian Wiki Vault
This folder is both a Claude Code plugin and an Obsidian vault.
**Plugin name:** `claude-obsidian` (v1.7+ "Compound Vault" — see [docs/compound-vault-guide.md](docs/compound-vault-guide.md); v1.8+ adds methodology modes — see [docs/methodology-modes-guide.md](docs/methodology-modes-guide.md))
**Skills:** `/wiki`, `/wiki-ingest`, `/wiki-query`, `/wiki-lint`, `/wiki-cli` (v1.7), `/wiki-retrieve` (v1.7, opt-in), `/wiki-mode` (v1.8)
**Vault path:** This directory (open in Obsidian directly)
## What This Vault Is For
This vault demonstrates the LLM Wiki pattern — a persistent, compounding knowledge base for Claude + Obsidian. Drop any source, ask any question, and the wiki grows richer with every session.
## Vault Structure
```
.raw/ source documents — immutable, Claude reads but never modifies
wiki/ Claude-generated knowledge base
_templates/ Obsidian Templater templates
_attachments/ images and PDFs referenced by wiki pages
```
## How to Use
Drop a source file into `.raw/`, then tell Claude: "ingest [filename]".
Ask any question. Claude reads the index first, then drills into relevant pages.
Run `/wiki` to scaffold a new vault or check setup status.
Run "lint the wiki" every 10-15 ingests to catch orphans and gaps.
## Cross-Project Access
To reference this wiki from another Claude Code project, add to that project's CLAUDE.md:
```markdown
## Wiki Knowledge Base
Path: /path/to/this/vault
When you need context not already in this project:
1. Read wiki/hot.md first (recent context, ~500 words)
2. If not enough, read wiki/index.md
3. If you need domain specifics, read wiki/<domain>/_index.md
4. Only then read individual wiki pages
Do NOT read the wiki for general coding questions or things already in this project.
```
## Plugin Skills
| Skill | Trigger |
|-------|---------|
| `/wiki` | Setup, scaffold, route to sub-skills |
| `ingest [source]` | Single or batch source ingestion |
| `query: [question]` | Answer from wiki content |
| `lint the wiki` | Health check |
| `/save` | File the current conversation as a structured wiki note |
| `/autoresearch [topic]` | Autonomous research loop: search, fetch, synthesize, file |
| `/canvas` | Visual layer: add images, PDFs, notes to Obsidian canvas |
| `/wiki-cli` (v1.7) | Obsidian CLI transport wrapper; default mutation path on desktop |
| `/wiki-retrieve` (v1.7) | Hybrid contextual + BM25 + cosine-rerank retrieval (opt-in via `bash bin/setup-retrieve.sh`) |
| `/wiki-mode` (v1.8) | Methodology modes (LYT / PARA / Zettelkasten / Generic). Set via `bash bin/setup-mode.sh`; consumed by wiki-ingest / save / autoresearch for routing new pages |
| `/think` (v1.9) | The 10-principle thinking loop (OBSERVE-OBSERVE-LISTEN-THINK-CONNECT-CONNECT-FEEL-ACCEPT-CREATE-GROW) as an invocable workflow. Apply to architectural decisions, audits, post-mortems, ambiguous user requests. Every other skill has a "How to think" appendix mapping this framework to its specific work |
## Transport (v1.7+)
`scripts/detect-transport.sh` writes `.vault-meta/transport.json` on first run and refreshes weekly. Skills consult it before mutating the vault. Fallback chain: Obsidian CLI → mcp-obsidian → mcpvault → filesystem (always-available floor). Decision tree: [wiki/references/transport-fallback.md](wiki/references/transport-fallback.md).
## Concurrency (v1.7+)
`scripts/wiki-lock.sh` provides per-file advisory locks for safe multi-writer ingest. Every wiki page write should be guarded by `wiki-lock acquire`/`release`. Stale-after default is 60s; cross-process release allowed by design. The PostToolUse hook defers `git add` while locks are held. Closes the latent multi-writer corruption hole from v1.6.
## Methodology Modes (v1.8+)
Pick an organizational style for the vault via `bash bin/setup-mode.sh`. Four modes available: **generic** (v1.7 default — no opinion), **LYT** (Linking Your Thinking — MOCs + atomic notes), **PARA** (Projects/Areas/Resources/Archives), **Zettelkasten** (timestamped IDs, flat, dense linking). The mode is written to `.vault-meta/mode.json` (gitignored by default; `git add -f` to commit). `wiki-ingest`, `save`, and `autoresearch` consult `python3 scripts/wiki-mode.py route <type> "<name>"` before filing new pages — no special-casing needed in the consumer skills. Full guide: [docs/methodology-modes-guide.md](docs/methodology-modes-guide.md). Closes priority gap 5 from the May 2026 compass artifact.
## Pre-commit verifier (v1.7.1+)
After staging changes for a non-trivial workstream but BEFORE running `git commit`, dispatch the `verifier` agent (`agents/verifier.md`). It reads `git diff --cached`, applies the /best-practices six-cut + agent kernel, and returns findings in four tiers (BLOCKER / HIGH / MEDIUM / LOW) with file:line citations. The agent has read-only tools (Read, Grep, Glob, Bash) — it can inspect but never modify, so its output is purely advisory. This closes the loop the v1.7 audit revealed: code went worker → commit with no separate verifier pass, which is how BLOCKER B1 (data-egress consent gap) slipped through. See `docs/audits/v1.7.0-audit-2026-05-17.md` §10 for the retrospective.
## MCP (Optional)
If you configured the MCP server, Claude can read and write vault notes directly.
See `skills/wiki/references/mcp-setup.md` for setup instructions.
## Release Blog Post
After cutting a new release (git tag + `gh release create`), run:
```
/release-blog
```
This generates a blog post on https://agricidaniel.com/blog/, handles cover image generation, SEO metadata, FAQ schema, internal linking, sitemap/llms.txt updates, Vercel deployment, and Google indexing.
CODEOWNERS
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# Default owner for everything
* @AgriciDaniel
CODE_OF_CONDUCT.md
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# Code of Conduct
This project adopts the [Contributor Covenant v2.1](https://www.contributor-covenant.org/version/2/1/code_of_conduct/) as its code of conduct.
## In short
- Be respectful and constructive.
- Assume good faith.
- Disagreement is welcome; personal attacks are not.
- Maintainers may remove comments, commits, or contributors that violate these standards.
## Reporting
Concerns about conduct can be reported privately to the maintainer at **agricidaniel@gmail.com**. Reports are confidential. Response within a reasonable timeframe.
For the full standard text (including specific examples of acceptable and unacceptable behavior, enforcement guidelines, and attribution), see the [Contributor Covenant homepage](https://www.contributor-covenant.org/).
CONTRIBUTING.md
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# Contributing to claude-obsidian
Thanks for your interest in improving this plugin. claude-obsidian is a small, focused project; contributions that match its philosophy land quickly.
## Philosophy
Three constraints shape every change:
1. **Read before write.** Every contribution starts by reading the affected files, their tests, and their callers. Removals break assumptions as often as additions.
2. **Smallest unit that works.** No speculative abstraction. Complexity is earned, not anticipated. Three real callers minimum before an abstraction lands.
3. **Failure is the spec.** Every new failure mode needs explicit handling. Untrusted input, network calls, and state changes need an explicit blast-radius answer.
The full kernel lives in [`/best-practices`](https://github.com/AgriciDaniel/best-practices) (composable Claude Code skill). The pre-commit verifier agent at [`agents/verifier.md`](agents/verifier.md) enforces it for non-trivial changes.
## Workflow
### 1. Open an issue first (for non-trivial changes)
For typo fixes, doc clarifications, or single-line changes, skip straight to a PR. For anything bigger:
- Open an issue using the bug-report or feature-request template
- Describe the problem, the proposed change, and the blast radius
- Wait for a thumbs-up before investing time
### 2. Fork + branch
Contributions are accepted on the public canonical repo. Fork [`AgriciDaniel/claude-obsidian`](https://github.com/AgriciDaniel/claude-obsidian) on GitHub, then:
```bash
git clone https://github.com/<your-username>/claude-obsidian.git
cd claude-obsidian
git checkout -b your-feature-name
```
> ℹ️ The public repo (`AgriciDaniel/claude-obsidian`) is the canonical source of truth. Raise all PRs against it. AI Marketing Hub Pro members working from the early-access mirror (`AI-Marketing-Hub/claude-obsidian`) should target the public canonical too, so contributions land in one place.
Branch names: `fix/...`, `feat/...`, `docs/...`, `refactor/...`.
### 3. Set up locally
The plugin runs anywhere Claude Code runs. For development:
```bash
# Run the hermetic test suite — required before submitting a PR
make test
# Optionally provision the v1.7 retrieval pipeline (requires consent for API egress)
bash bin/setup-retrieve.sh
# Optionally pick a methodology mode for testing the v1.8 routing
bash bin/setup-mode.sh
```
### 4. Make the change
Follow the six-cut kernel:
- Read every file you're touching
- Name new identifiers like the next reader is hostile
- Smallest unit that works
- Delete more than you add (when superseding)
- Evidence over intuition (tests for new behavior)
- Failure-mode + undo plan documented
If you add a new skill, agent, script, or hook, also add a test under `tests/`. The 9 hermetic test suites are the project's safety net.
### 5. Run the tests
```bash
make test
```
All 9 suites must pass (~1240 assertions). Tests are hermetic: no network, no ollama, no Anthropic API. If your change adds a network call, gate it behind a `--consent`/`--allow-egress`/env-var pattern matching `scripts/contextual-prefix.py` or `scripts/tiling-check.py`.
### 6. Run the verifier (optional but recommended)
For multi-file changes:
```bash
# After git add, before git commit, dispatch the verifier agent
# (Claude Code: invoke agents/verifier.md on the staged diff)
```
The verifier applies the six-cut + agent kernel to your staged diff and returns findings in BLOCKER / HIGH / MEDIUM / LOW tiers. Address BLOCKER + HIGH before committing.
### 7. Commit
Commit message convention (Conventional Commits):
```
<type>(<scope>): <short description>
<longer body if needed>
```
Types: `feat`, `fix`, `docs`, `chore`, `refactor`, `test`, `perf`, `style`.
Example:
```
fix(wiki-mode): close path-traversal in route_path safe_name
Sanitize routing input via safe_name() before string-concat into
the vault-relative path. Adds 9 hermetic test assertions for traversal
vectors. Closes audit finding S1.
```
### 8. Update CHANGELOG.md
Add an entry under `## [Unreleased]` (create the section if needed). Follow the [Keep a Changelog](https://keepachangelog.com/en/1.1.0/) format:
```markdown
## [Unreleased]
### Added
- Description of new feature
### Fixed
- Description of bug fix
```
The maintainer will move your entry to a versioned section at release time.
### 9. Open a PR
Use the PR template. Required fields:
- What changed
- Why
- How it was tested (paste `make test` output if relevant)
- Audit/verifier results if applicable
PRs are reviewed against the kernel. Expect feedback on naming, scope, and failure-mode coverage.
## Testing standards
- **Hermetic.** No network, no external services, no user-specific environment.
- **Fast.** The full suite runs in under a minute.
- **Deterministic.** Same input → same output, every time.
- **Documented.** Every test asserts a named behavior, not a coincidence.
If you can't make your test hermetic, ask in the issue whether a mocked alternative is acceptable.
## What we will NOT merge
- Code without tests for new behavior
- Speculative abstractions (no real callers yet)
- Network calls without an explicit consent gate
- Path construction from user input without sanitization (see `scripts/wiki-mode.py:safe_name`)
- Skills/agents that shell out without documenting the failure mode
- Anything that breaks the existing test suite without a documented reason
## Security
Found a vulnerability? Do NOT open a public issue. See [SECURITY.md](SECURITY.md) for disclosure.
## License
By contributing, you agree your contributions are licensed under the [MIT License](LICENSE).
## Code of Conduct
Participation is governed by the [Contributor Covenant Code of Conduct](CODE_OF_CONDUCT.md).
GEMINI.md
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# claude-obsidian: Gemini CLI Instructions
This repo is a knowledge base companion that builds persistent, compounding Obsidian wiki vaults using Andrej Karpathy's LLM Wiki pattern. The skills are written in the cross-platform Agent Skills format and work in Gemini CLI / Antigravity alongside Claude Code.
## Skills Discovery
Skills live in `skills/<name>/SKILL.md`. To make them available to Gemini CLI:
```bash
ln -s "$(pwd)/skills" ~/.gemini/skills/claude-obsidian
```
Or run the bundled installer:
```bash
bash bin/setup-multi-agent.sh
```
## Skills
| Skill | What it does |
|---|---|
| `wiki` | Scaffolds a new vault, manages hot cache, routes to sub-skills |
| `wiki-ingest` | Reads sources (files, URLs, images) and creates 8-15 wiki pages each |
| `wiki-query` | Answers questions from the wiki with three depth modes |
| `wiki-lint` | Health checks: orphans, dead links, stale claims, gaps |
| `save` | Files the current conversation as a wiki note |
| `autoresearch` | Autonomous research loop: search → fetch → synthesize → file |
| `canvas` | Creates and edits Obsidian canvas (.canvas) files |
| `defuddle` | Cleans web pages before ingest (saves 40-60% tokens) |
| `obsidian-markdown` | Obsidian Flavored Markdown syntax reference |
| `obsidian-bases` | Obsidian Bases (.base files): native database views |
## Trigger Phrases (Examples)
- "set up wiki" → `wiki`
- "ingest this article" → `wiki-ingest`
- "ingest https://example.com/article" → `wiki-ingest` (URL mode)
- "what do you know about X" → `wiki-query`
- "lint the wiki" → `wiki-lint`
- "save this conversation" → `save`
- "research [topic]" → `autoresearch`
## Vault Conventions
- `.raw/`: source documents, immutable (never modify)
- `wiki/`: agent-generated knowledge (you own this)
- `wiki/hot.md`: recent context cache (~500 tokens), read first at session start
- `wiki/index.md`: master catalog
- `.raw/.manifest.json`: delta tracking for ingest
## Bootstrap
On first session:
1. Read this file + the project `CLAUDE.md`
2. If `wiki/hot.md` exists, silently read it to restore recent context
3. Wait for user to type `/wiki` or `ingest` or `query`
## Project Links
- Plugin (public canonical): https://github.com/AgriciDaniel/claude-obsidian
- Community early-access mirror (Pro): https://github.com/AI-Marketing-Hub
- Pattern: https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f
LICENSE
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MIT License
Copyright (c) 2026 AgriciDaniel (AI Marketing Hub)
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
Makefile
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# claude-obsidian Makefile
# Test runner entry points for DragonScale and vault tooling.
.PHONY: test test-address test-tiling test-boundary test-bm25 test-retrieve \
test-lock test-concurrent test-mode test-contextual setup-dragonscale \
setup-retrieve setup-mode clean-test-state help
help:
@echo "claude-obsidian developer targets:"
@echo " make test Run all v1.7 tests (DragonScale + retrieval + concurrency)"
@echo " make test-address scripts/allocate-address.sh tests (shell)"
@echo " make test-tiling scripts/tiling-check.py tests (python, no ollama required)"
@echo " make test-boundary scripts/boundary-score.py tests (python, no prereqs)"
@echo " make test-bm25 scripts/bm25-index.py tests (python, hermetic)"
@echo " make test-retrieve scripts/retrieve.py + rerank.py tests (python, hermetic)"
@echo " make test-lock scripts/wiki-lock.sh tests (shell, hermetic)"
@echo " make test-concurrent multi-writer correctness gate (shell, hermetic)"
@echo " make test-mode scripts/wiki-mode.py tests (python, hermetic)"
@echo " make test-contextual scripts/contextual-prefix.py cache-floor tests (python, hermetic)"
@echo " make setup-dragonscale Run bin/setup-dragonscale.sh against this vault"
@echo " make setup-retrieve Run bin/setup-retrieve.sh against this vault (opt-in v1.7)"
@echo " make setup-mode Run bin/setup-mode.sh to pick a methodology mode (opt-in v1.8)"
@echo " make clean-test-state Remove runtime lockfiles and tiling/embed caches"
test: test-address test-tiling test-boundary test-bm25 test-retrieve test-lock test-concurrent test-mode test-contextual
@echo ""
@echo "All tests passed."
test-address:
@echo "=== test_allocate_address.sh ==="
@bash tests/test_allocate_address.sh
test-tiling:
@echo "=== test_tiling_check.py ==="
@python3 tests/test_tiling_check.py
test-boundary:
@echo "=== test_boundary_score.py ==="
@python3 tests/test_boundary_score.py
test-bm25:
@echo "=== test_bm25_index.py ==="
@python3 tests/test_bm25_index.py
test-retrieve:
@echo "=== test_retrieve.py ==="
@python3 tests/test_retrieve.py
test-lock:
@echo "=== test_wiki_lock.sh ==="
@bash tests/test_wiki_lock.sh
test-concurrent:
@echo "=== test_concurrent_write.sh ==="
@bash tests/test_concurrent_write.sh
test-mode:
@echo "=== test_wiki_mode.py ==="
@python3 tests/test_wiki_mode.py
test-contextual:
@echo "=== test_contextual_prefix.py ==="
@python3 tests/test_contextual_prefix.py
setup-dragonscale:
@bash bin/setup-dragonscale.sh
setup-retrieve:
@bash bin/setup-retrieve.sh
setup-mode:
@bash bin/setup-mode.sh
clean-test-state:
@rm -f .vault-meta/.address.lock .vault-meta/.tiling.lock .vault-meta/.bm25.lock \
.vault-meta/.embed-cache.lock .vault-meta/.wiki-lock.meta \
.vault-meta/tiling-cache.json \
.vault-meta/tiling-cache.*.tmp .vault-meta/embed-cache.json \
.vault-meta/embed-cache.*.tmp .vault-meta/transport.json \
.vault-meta/transport.*.tmp
@rm -rf .vault-meta/chunks/ .vault-meta/bm25/ .vault-meta/locks/
@rm -f .vault-meta/mode.json .vault-meta/mode.*.tmp .vault-meta/hook.log
@echo "Runtime lockfiles, caches, and v1.7/v1.8 runtime artifacts removed."
PRIVACY.md
+39
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@@ -0,0 +1,39 @@
# Privacy
## Data Handling
claude-obsidian is a Claude Code plugin and Obsidian vault that runs entirely on
your local machine. Your vault is plain Markdown on your own filesystem. The core
skill does not collect, transmit, or store any personal data, and there is no
telemetry, analytics, or usage tracking.
## What Stays Local
- Ingesting sources, answering queries, linting, and updating the hot cache all
run inside your local Claude Code session.
- All wiki content (`wiki/`) is plain Markdown saved to your local filesystem.
- The `/wiki-retrieve` BM25 index and optional ollama-based reranking run fully
locally. Without an explicit opt-in flag, retrieval never leaves your machine.
## Optional Network Egress (opt-in, consent-gated)
Network calls happen only when you explicitly enable them. By default everything
is local.
| Feature | Service | Data sent | Gate |
|---------|---------|-----------|------|
| `/wiki-retrieve` contextual prefix | Anthropic API | Wiki page chunks (for prefix generation) | Off by default. Requires the `--allow-egress` consent flag on `scripts/contextual-prefix.py`; without it, the tier falls back to `claude` on PATH or a fully local synthetic prefix. |
| `/autoresearch` | Web search + fetch | Your research query and fetched URLs | Opt-in; only runs when you invoke the research loop. |
| `/defuddle` | Web fetch | URLs you ask it to extract | Opt-in; only runs when you invoke it. |
| ollama rerank | `localhost` only | Query + candidate chunks | Local by default. Remote ollama hosts are refused unless you pass `--allow-remote-ollama`. |
## Credentials
- API keys (such as `ANTHROPIC_API_KEY`) are read from environment variables or
your local `.env`, never hard-coded.
- Credentials are never committed to the repository (blocked by `.gitignore`).
- The included demo vault and configuration ship with placeholder values only.
## Security Disclosure
To report a security or privacy issue, see [`SECURITY.md`](SECURITY.md).
README.md
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@@ -0,0 +1,676 @@
# claude-obsidian: Self-Organizing AI Second Brain for Obsidian + Claude Code
<p align="center">
<img src="wiki/meta/claude-obsidian-gif-cover-16x9.gif" alt="claude-obsidian: persistent compounding wiki vault for Claude Code and Obsidian" width="100%" />
</p>
[![GitHub stars](https://img.shields.io/github/stars/AgriciDaniel/claude-obsidian?style=flat&color=e8734a)](https://github.com/AgriciDaniel/claude-obsidian/stargazers)
[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](LICENSE)
[![Release](https://img.shields.io/github/v/release/AgriciDaniel/claude-obsidian?color=blue)](https://github.com/AgriciDaniel/claude-obsidian/releases/latest)
[![CI](https://github.com/AgriciDaniel/claude-obsidian/actions/workflows/test.yml/badge.svg)](https://github.com/AgriciDaniel/claude-obsidian/actions/workflows/test.yml)
[![Claude Code](https://img.shields.io/badge/Claude_Code-plugin-8B5CF6)](https://code.claude.com/docs/en/discover-plugins)
[![Obsidian](https://img.shields.io/badge/Obsidian-v1.9.10%2B-7c3aed)](https://obsidian.md)
[![Agent Skills](https://img.shields.io/badge/Agent%20Skills-Compatible-blue)](https://agentskills.io)
[![Community](https://img.shields.io/badge/AI%20Marketing%20Hub-Pro%20community-purple)](https://www.skool.com/ai-marketing-hub-pro)
[![Blog Post](https://img.shields.io/badge/Deep_Dive-Blog_Post-22c55e)](https://agricidaniel.com/blog/claude-obsidian-ai-second-brain)
Claude + Obsidian knowledge companion and self-organizing AI second brain. A running AI notetaker that builds and maintains a persistent, compounding wiki vault. Every source you add gets integrated. Every question you ask pulls from everything that has been read. Knowledge compounds like interest.
Open-source Obsidian AI plugin for AI note-taking, personal knowledge management (PKM), second-brain workflows, and a private Notion alternative. **15 Claude Code skills**, multi-agent support, multi-writer safe (v1.7+), first-class methodology modes (LYT / PARA / Zettelkasten / Generic via v1.8), and the 10-principle thinking framework (v1.9). Based on [Andrej Karpathy's LLM Wiki pattern](https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f).
> **Two ways to get this skill.** Pick the one that fits how you work.
>
> - 🌐 **Public open-source build** (latest: `v1.9.2`, recommended): the free, MIT-licensed release on [Daniel Agrici's GitHub](https://github.com/AgriciDaniel/claude-obsidian). Open to anyone, no membership required. Ships everything: v1.7 Compound Vault, v1.8 methodology modes, and the v1.9 thinking framework plus audit hardening.
> - ⚡ **AI Marketing Hub Pro**: the same MIT-licensed core, plus earliest access to in-development features before they land here, direct collaboration, and the [Pro community](https://www.skool.com/ai-marketing-hub-pro). Pro members install from the [AI Marketing Hub](https://github.com/AI-Marketing-Hub) org mirror (swap note under Option 2 below).
> ✨ **v1.7 "Compound Vault" refoundation**: Obsidian CLI as default transport, hybrid retrieval (contextual prefix + BM25 + cosine rerank per [Anthropic's Sept 2024 research](https://www.anthropic.com/news/contextual-retrieval)), per-file advisory locking that closes a latent multi-writer corruption hole, and substrate alignment with [kepano/obsidian-skills](https://github.com/kepano/obsidian-skills). Full guide: [docs/compound-vault-guide.md](docs/compound-vault-guide.md). Optional [DragonScale Memory](docs/dragonscale-guide.md) extension (log folds, deterministic page addresses, semantic tiling lint, boundary-first autoresearch).
---
## Contents
- [What It Does](#what-it-does)
- [Why claude-obsidian?](#why-claude-obsidian)
- [Quick Start](#quick-start)
- [Commands](#commands)
- [`/wiki`: setup, scaffold, continue](#wiki-setup-scaffold-continue)
- [`/autoresearch`: autonomous research loop](#autoresearch-autonomous-research-loop)
- [`/canvas`: visual layer](#canvas-visual-layer)
- [`/think`: 10-principle thinking loop](#think-10-principle-thinking-loop)
- [Methodology Modes (v1.8+)](#methodology-modes-v18)
- [Vault Use Cases (v1.0+)](#vault-use-cases-v10)
- [Cross-Project Knowledge Base](#cross-project-knowledge-base)
- [What Gets Created](#what-gets-created)
- [Architecture](#architecture)
- [MCP Setup (Optional)](#mcp-setup-optional)
- [Plugins](#plugins)
- [CSS Snippets](#css-snippets-auto-enabled-by-setup-vaultsh)
- [Banner Plugin](#banner-plugin)
- [File Structure](#file-structure)
- [AutoResearch Configuration](#autoresearch-programmd)
- [Seed Vault](#seed-vault)
- [Companion: claude-canvas](#companion-claude-canvas)
- [FAQ](#faq)
- [Requirements](#requirements)
- [Uninstall](#uninstall)
- [Contributing](#contributing)
- [Related Projects](#related-projects)
- [Community](#community)
- [License](#license)
---
## What It Does
### [YouTube Demo](https://www.youtube.com/watch?v=a2hgayvr-H4)
<p align="center">
<img src="wiki/meta/welcome-canvas.gif" alt="claude-obsidian welcome canvas: visual demo of the wiki vault workflow" width="96%" />
</p>
You drop sources. Claude reads them, extracts entities and concepts, updates cross-references, and files everything into a structured Obsidian vault. The wiki gets richer with every ingest.
You ask questions. Claude reads the hot cache (recent context), scans the index, drills into relevant pages, and synthesizes an answer. It cites specific wiki pages, not training data.
You lint. Claude finds orphans, dead links, stale claims, and missing cross-references. Your wiki stays healthy without manual cleanup.
At the end of every session, Claude updates a hot cache. The next session starts with full recent context, no recap needed.
<p align="center">
<img src="wiki/meta/image-example-graph-view.png" alt="Obsidian graph view showing the claude-obsidian knowledge graph with color-coded nodes for concepts, entities, and sources" width="48%" />
<img src="wiki/meta/image-example-wiki-map-view.png" alt="Wiki Map canvas: visual hub linking domain pages, concepts, and entities" width="48%" />
</p>
---
## Why claude-obsidian?
Most Obsidian AI plugins are chat interfaces. They answer questions about your existing notes. claude-obsidian is a knowledge engine. It creates, organizes, maintains, and evolves your notes autonomously.
| Capability | claude-obsidian | Smart Connections | Copilot |
|---|---|---|---|
| **Auto-organize notes** | ✅ Creates entities, concepts, cross-references | ❌ | ❌ |
| **Contradiction flagging** | ✅ `[!contradiction]` callouts with sources | ❌ | ❌ |
| **Session memory** | ✅ Hot cache persists between conversations | ❌ | ❌ |
| **Vault maintenance** | ✅ 8-category lint (orphans, dead links, gaps) | ❌ | ❌ |
| **Autonomous research** | ✅ 3-round web research with gap-filling | ❌ | ❌ |
| **Methodology modes** | ✅ LYT / PARA / Zettelkasten / Generic (first-class) | ❌ | ❌ |
| **Thinking framework** | ✅ 10-principle loop as invocable skill | ❌ | ❌ |
| **Multi-model support** | ✅ Claude, Gemini, Codex, Cursor, Windsurf | ❌ Claude only | ✅ Multiple |
| **Visual canvas** | ✅ Via [claude-canvas](https://github.com/AgriciDaniel/claude-canvas) | ❌ | ❌ |
| **Multi-writer safe** | ✅ Per-file advisory locks (v1.7+) | ❌ | ❌ |
| **Query with citations** | ✅ Cites specific wiki pages | ✅ Cites similar notes | ✅ Cites notes |
| **Batch ingestion** | ✅ Parallel agents for multiple sources | ❌ | ❌ |
| **Open source** | ✅ MIT | ✅ MIT | ⚠️ Freemium |
> 📖 **Deep dive:** [I Turned Obsidian Into a Self-Organizing AI Brain](https://agricidaniel.com/blog/claude-obsidian-ai-second-brain). Full breakdown with data visualizations, market context, and workflow demos.
---
## Quick Start
> ℹ️ The commands below install the **public open-source build** from `AgriciDaniel/claude-obsidian` (recommended, no membership needed). **AI Marketing Hub Pro members** who want early access to in-development features can swap `AgriciDaniel/claude-obsidian` for `AI-Marketing-Hub/claude-obsidian` (Option 2 also swaps the plugin slug; see the note under that option).
### Option 1: Clone as vault (recommended, full setup in 2 minutes)
```bash
git clone https://github.com/AgriciDaniel/claude-obsidian
cd claude-obsidian
bash bin/setup-vault.sh
```
Open the folder in Obsidian: **Manage Vaults → Open folder as vault → select `claude-obsidian/`**.
Open Claude Code in the same folder. Type `/wiki`.
> ℹ️ `setup-vault.sh` configures `graph.json` (filter + colors), `app.json` (excludes plugin dirs), and `appearance.json` (enables CSS). Run it once before the first Obsidian open. You get the fully pre-configured graph view, color scheme, and wiki structure out of the box.
---
### Option 2: Install as Claude Code plugin
Plugin installation is a two-step process. First add the marketplace catalog, then install the plugin from it.
> ℹ️ **Which version are you installing?**
>
> - **Public (recommended, no membership):** the commands below install the free, MIT-licensed release from [`AgriciDaniel/claude-obsidian`](https://github.com/AgriciDaniel/claude-obsidian). Nothing to sign up for.
> - **AI Marketing Hub Pro member?** For early access to in-development features, swap `AgriciDaniel/claude-obsidian` for `AI-Marketing-Hub/claude-obsidian` and the plugin slug `claude-obsidian@agricidaniel-claude-obsidian` for `claude-obsidian@ai-marketing-hub-claude-obsidian`. The org mirror requires an authenticated `gh auth login` (or GitHub PAT) with access to the `AI-Marketing-Hub` org. If `/plugin marketplace add` returns a 404, your account is not in the org yet. DM in the [Skool community](https://www.skool.com/ai-marketing-hub-pro) to get added.
```bash
# Step 1: add the marketplace
claude plugin marketplace add AgriciDaniel/claude-obsidian
# Step 2: install the plugin
claude plugin install claude-obsidian@agricidaniel-claude-obsidian
```
In any Claude Code session: `/wiki`. Claude walks you through vault setup.
To check it worked:
```bash
claude plugin list
```
---
### Option 3: Add to an existing vault
Copy `WIKI.md` into your vault root. Paste into Claude:
```
Read WIKI.md in this project. Then:
1. Check if Obsidian is installed. If not, install it.
2. Check if the Local REST API plugin is running on port 27124.
3. Configure the MCP server.
4. Ask me ONE question: "What is this vault for?"
Then scaffold the full wiki structure.
```
---
## Commands
| You say | Claude does |
|---------|------------|
| `/wiki` | Setup check, scaffold, or continue where you left off |
| `ingest [file]` | Read source, create 8-15 wiki pages, update index and log |
| `ingest all of these` | Batch process multiple sources, then cross-reference |
| `what do you know about X?` | Read index, drill into relevant pages, synthesize answer |
| `/save` | File the current conversation as a wiki note |
| `/save [name]` | Save with a specific title (skips the naming question) |
| `/autoresearch [topic]` | Run the autonomous research loop: search, fetch, synthesize, file |
| `/canvas` | Open or create the visual canvas, list zones and nodes |
| `/canvas add image [path]` | Add an image (URL or local path) to the canvas with auto-layout |
| `/canvas add text [content]` | Add a markdown text card to the canvas |
| `/canvas add pdf [path]` | Add a PDF document as a rendered preview node |
| `/canvas add note [page]` | Pin a wiki page as a linked card on the canvas |
| `/canvas zone [name]` | Add a new labeled zone to organize visual content |
| `/canvas from banana` | Capture recently generated images onto the canvas |
| `/think [problem]` | Apply the 10-principle thinking loop to a non-trivial problem |
| `lint the wiki` | Health check: orphans, dead links, gaps, suggestions |
| `update hot cache` | Refresh hot.md with latest context summary |
> ✨ **Want more?** [claude-canvas](https://github.com/AgriciDaniel/claude-canvas) adds 12 templates, 6 layout algorithms, AI image generation, presentations, and full canvas orchestration. Install both, they complement each other.
### `/wiki`: setup, scaffold, continue
First-run setup walks through:
1. Check Obsidian is installed
2. Check Local REST API plugin (if MCP transport desired)
3. Ask "What is this vault for?" (one question, drives the scaffold)
4. Scaffold per chosen [Methodology Mode](#methodology-modes-v18) and [Vault Use Case](#vault-use-cases-v10)
5. Seed `hot.md`, `index.md`, `log.md`, `wiki/meta/dashboard.base`
6. Suggest the first ingest
On subsequent runs, `/wiki` continues where you left off. It checks vault health, surfaces stale claims, and shows recent activity from `hot.md`.
### `/autoresearch`: autonomous research loop
Configurable program at [`skills/autoresearch/references/program.md`](skills/autoresearch/references/program.md):
- Max rounds (default 3)
- Max pages per session (default 15)
- Source preference rules (academic, official docs, news)
- Confidence scoring + domain constraints
The loop:
1. **Round 1, broad search**: decompose into 3-5 angles, run 2-3 queries per angle, fetch top 2-3 results per angle
2. **Round 2, gap fill**: targeted searches for contradictions and missing pieces
3. **Round 3, synthesis check** (optional): one more pass if major gaps remain
4. **Filing**: synthesis page + source pages + entity pages + concept pages, all cross-referenced
URL validation + content sanitization applied per the `## Web egress hygiene (v1.8.2+)` policy in [`skills/autoresearch/SKILL.md`](skills/autoresearch/SKILL.md): rejects `file://` / `javascript:` / RFC1918 hosts, strips `<script>` and wikilink-injection attempts, caps fetch bodies at 50KB.
### `/canvas`: visual layer
Add images, PDFs, notes, and AI-generated images to an Obsidian canvas. Zone management for grouping. Auto-layout positions nodes without overlap.
```
/canvas # open or create the canvas
/canvas add image <path> # add an image with auto-layout
/canvas add pdf <path> # render PDF as preview node
/canvas add note <wiki-page> # pin a wiki page as a linked card
/canvas zone <name> # add a labeled zone
/canvas from banana # capture recent banana-generated images
```
JSON Canvas 1.0 spec compliant ([`skills/canvas/references/canvas-spec.md`](skills/canvas/references/canvas-spec.md)). Full orchestration (12 templates, 6 layout algorithms, presentations) in the companion [claude-canvas](https://github.com/AgriciDaniel/claude-canvas).
### `/think`: 10-principle thinking loop
Apply the OBSERVE-OBSERVE-LISTEN-THINK-CONNECT-CONNECT-FEEL-ACCEPT-CREATE-GROW framework to any non-trivial problem (architectural decisions, audits, post-mortems, ambiguous user requests).
```
/think <problem statement>
```
The framework walks Claude through 10 stages with prompts at each. Use when problem novelty + irreversibility justify the discipline. See [`skills/think/SKILL.md`](skills/think/SKILL.md) for the full framework. Every other skill has a "How to think" appendix mapping the framework to its specific work. The [v1.8.0 pre-push audit](docs/audits/v1.8.0-pre-push-audit-2026-05-18.md) used this framework as its methodology spine.
---
## Methodology Modes (v1.8+)
Four organizational philosophies, opt-in via `bash bin/setup-mode.sh`. The `wiki-mode` skill (v1.8+) reads `.vault-meta/mode.json` and routes new pages accordingly. Default is `generic` (v1.7 behavior, no opinion imposed).
| Mode | Philosophy | Filing convention |
|------|-----------|-------------------|
| **Generic** (default) | No opinion. v1.7 behavior preserved. | `wiki/sources/`, `wiki/entities/`, `wiki/concepts/`, `wiki/sessions/` |
| **LYT** (Linking Your Thinking) | Notes link, folders don't. MOCs are the navigation primitive. | `wiki/mocs/<topic>-moc.md` + `wiki/notes/<atomic-note>.md` |
| **PARA** (Tiago Forte) | Organize by actionability (Projects, Areas, Resources, Archives). | `wiki/projects/`, `wiki/areas/`, `wiki/resources/`, `wiki/archives/` |
| **Zettelkasten** (Luhmann slip-box) | Atomic notes, unique IDs, dense bidirectional linking, no folders. | `wiki/<YYYYMMDDHHMMSSffffff>-<slug>.md` (flat, timestamped) |
Switching modes does NOT auto-migrate existing files. Full guide: [`docs/methodology-modes-guide.md`](docs/methodology-modes-guide.md).
---
## Vault Use Cases (v1.0+)
These describe **what** your vault is for. They compose with Methodology Modes (which describe **how** it is organized).
| Use case | When to use |
|----------|-------------|
| **A: Website** | Sitemap, content audit, SEO wiki |
| **B: GitHub** | Codebase map, architecture wiki |
| **C: Business** | Project wiki, competitive intelligence |
| **D: Personal** | Second brain, goals, journal synthesis |
| **E: Research** | Papers, concepts, thesis |
| **F: Book/Course** | Chapter tracker, course notes |
Use cases can be combined. A Business + Research vault organized in PARA is a valid composition.
---
## Cross-Project Knowledge Base
Point any Claude Code project at this vault. Add to that project's `CLAUDE.md`:
```markdown
## Wiki Knowledge Base
Path: ~/path/to/vault
When you need context not already in this project:
1. Read wiki/hot.md first (recent context cache)
2. If not enough, read wiki/index.md
3. If you need domain details, read the relevant domain sub-index
4. Only then drill into specific wiki pages
Do NOT read the wiki for general coding questions or tasks unrelated to [domain].
```
Your executive assistant, coding projects, and content workflows all draw from the same knowledge base.
---
## What Gets Created
A typical scaffold creates:
- Folder structure for your chosen use case + methodology mode
- `wiki/index.md`: master catalog
- `wiki/log.md`: append-only operation log
- `wiki/hot.md`: recent context cache
- `wiki/overview.md`: executive summary
- `wiki/meta/dashboard.base`: Bases dashboard (primary, native Obsidian)
- `wiki/meta/dashboard.md`: Legacy Dataview dashboard (optional fallback)
- `_templates/`: Obsidian Templater templates for each note type
- `.obsidian/snippets/vault-colors.css`: color-coded file explorer
- Vault `CLAUDE.md`: auto-loaded project instructions
---
## Architecture
Three diagrams explain the substantive design choices of the plugin.
### Vault flow
Sources land in `.raw/`. The `/wiki-ingest` agent reads each source, extracts entities and concepts, files them into the appropriate `wiki/` subfolder (per active methodology mode), and updates the index, log, and hot cache. Queries read hot → index → pages in that order to keep token cost low.
<p align="center">
<img src="assets/diagrams/vault-flow.svg" alt="Architecture diagram: sources flow into the wiki-ingest agent, which produces entity, concept, and source pages. The index and hot cache are updated. The wiki-query interface reads the cache, index, and pages to synthesize cited answers." width="100%" />
</p>
### Multi-writer safety (v1.7+)
Parallel ingest sub-agents can target the same wiki page if the user batches multiple sources. `scripts/wiki-lock.sh` provides per-file advisory locks: one writer acquires, the other waits and retries on the next pass. The PostToolUse auto-commit hook checks the lock list before staging, deferring the commit while writes are in flight.
<p align="center">
<img src="assets/diagrams/multi-writer-locking.svg" alt="Architecture diagram: two parallel writers attempt to acquire a lock on the same wiki page via wiki-lock.sh. One writer is granted, writes the page, and releases the lock. The other writer logs the skip and retries on the next pass. No corruption, no half-written pages." width="100%" />
</p>
### Hybrid retrieval (v1.7+, opt-in)
The `/wiki-retrieve` skill ships a three-tier retrieval pipeline based on [Anthropic's Sept 2024 contextual retrieval research](https://www.anthropic.com/news/contextual-retrieval). BM25 is the always-on sparse layer. The contextual-prefix tier is consent-gated (`--allow-egress`) for users who want to send page bodies to the Anthropic API for prefix generation. Cosine rerank uses a local ollama model by default. The 50-query benchmark in v1.7 measured +32 percentage points top-1 accuracy and +41 percent error reduction vs the v1.6 baseline.
<p align="center">
<img src="assets/diagrams/hybrid-retrieval.svg" alt="Architecture diagram: user query feeds both BM25 sparse search and an optional contextual-prefix Anthropic API call. Both feed a cosine rerank via local ollama embeddings. The output is a ranked list of candidates with --explain traceability for every score." width="100%" />
</p>
> ℹ️ Provision the pipeline with `bash bin/setup-retrieve.sh`. It builds the BM25 index, prompts for egress consent, and validates the ollama connection. The pipeline degrades gracefully: if any tier is unavailable, the rest still return useful results.
---
## MCP Setup (Optional)
MCP lets Claude read and write vault notes directly without copy-paste.
**Option A (REST API based):**
1. Install the Local REST API plugin in Obsidian
2. Copy your API key
3. Run:
```bash
claude mcp add-json obsidian-vault '{
"type": "stdio",
"command": "uvx",
"args": ["mcp-obsidian"],
"env": {
"OBSIDIAN_API_KEY": "your-key",
"OBSIDIAN_HOST": "127.0.0.1",
"OBSIDIAN_PORT": "27124",
"NODE_TLS_REJECT_UNAUTHORIZED": "0"
}
}' --scope user
```
**Option B (filesystem based, no plugin needed):**
```bash
claude mcp add-json obsidian-vault '{
"type": "stdio",
"command": "npx",
"args": ["-y", "@bitbonsai/mcpvault@latest", "/path/to/your/vault"]
}' --scope user
```
> ℹ️ Both transports are auto-detected by `scripts/detect-transport.sh`. The result lands in `.vault-meta/transport.json`. To pin a manual choice, edit that file and set `"manual_override": true` (v1.8.2+ honors it).
---
## Plugins
### Core Plugins (built into Obsidian, no install needed)
| Plugin | Purpose |
|--------|---------|
| **Bases** | Powers `wiki/meta/dashboard.base`: native database views. Available since Obsidian v1.9.10 (August 2025). Replaces Dataview for the primary dashboard. |
| **Properties** | Visual frontmatter editor |
| **Backlinks**, **Outline**, **Graph view** | Standard navigation |
### Pre-installed Community Plugins (ship with this vault)
Enable in **Settings → Community Plugins → enable**:
| Plugin | Purpose | Notes |
|--------|---------|-------|
| **Calendar** | Right-sidebar calendar with word count + task dots | Pre-installed |
| **Thino** | Quick memo capture panel | Pre-installed |
| **Excalidraw** | Freehand drawing canvas, annotate images | Pre-installed* |
| **Banners** | Notion-style header image via `banner:` frontmatter | Pre-installed |
\* Excalidraw `main.js` (8MB) is downloaded automatically by `setup-vault.sh`. It is not tracked in git.
### Also install from Community Plugins (not pre-installed)
| Plugin | Purpose |
|--------|---------|
| **Templater** | Auto-fills frontmatter from `_templates/` |
| **Obsidian Git** | Auto-commits vault every 15 minutes |
| **Dataview** *(optional, legacy)* | Only needed for the legacy `wiki/meta/dashboard.md` queries. The primary dashboard now uses Bases. |
Also install the **[Obsidian Web Clipper](https://obsidian.md/clipper)** browser extension. Sends web pages to `.raw/` in one click.
---
## CSS Snippets (auto-enabled by setup-vault.sh)
Three snippets ship with the vault and are enabled automatically:
| Snippet | Effect |
|---------|--------|
| `vault-colors` | Color-codes `wiki/` folders by type in the file explorer (blue = concepts, green = sources, purple = entities) |
| `ITS-Dataview-Cards` | Turns Dataview `TABLE` queries into visual card grids: use ` ```dataviewjs ` with `.cards` class |
| `ITS-Image-Adjustments` | Fine-grained image sizing in notes: append `\|100` to any image embed |
---
## Banner Plugin
Add to any wiki page frontmatter:
```yaml
banner: "_attachments/images/your-image.png"
banner_icon: "🧠"
```
The page renders a full-width header image in Obsidian. Works great for hub pages and overviews.
---
## File Structure
```
claude-obsidian/
├── .claude-plugin/
│ ├── plugin.json # manifest
│ └── marketplace.json # distribution
├── skills/ # 15 Claude Code skills (v1.9.2)
│ ├── wiki/ # orchestrator + references
│ ├── wiki-ingest/ # source ingestion
│ ├── wiki-query/ # answer questions from the vault
│ ├── wiki-lint/ # vault health check
│ ├── wiki-cli/ # Obsidian CLI transport (v1.7+)
│ ├── wiki-retrieve/ # hybrid retrieval (v1.7+, opt-in)
│ ├── wiki-mode/ # methodology modes router (v1.8+)
│ ├── wiki-fold/ # log rollup (DragonScale opt-in)
│ ├── save/ # /save: file conversations to wiki
│ ├── autoresearch/ # autonomous research loop
│ ├── canvas/ # visual layer (images, PDFs, notes)
│ ├── defuddle/ # web extraction wrapper
│ ├── obsidian-bases/ # Bases schema reference
│ ├── obsidian-markdown/ # OFM syntax reference
│ └── think/ # 10-principle thinking framework (v1.9+)
├── agents/
│ ├── verifier.md # pre-commit audit agent (v1.7.1+)
│ ├── wiki-ingest.md # parallel batch ingestion agent
│ └── wiki-lint.md # health check agent
├── commands/ # slash command entry points
├── hooks/
│ └── hooks.json # SessionStart + Stop + PostToolUse hooks
├── scripts/ # 12 helper scripts (transport, locking, retrieval, etc.)
├── tests/ # 9 hermetic test suites (~1240 assertions, make test)
├── bin/ # 5 setup scripts (setup-vault, setup-retrieve, setup-mode, etc.)
├── _templates/ # Obsidian Templater templates
├── wiki/ # seeded vault content (demo)
│ ├── canvases/ # welcome.canvas + main.canvas
│ ├── concepts/ # seeded: LLM Wiki Pattern, Hot Cache, Compounding Knowledge
│ ├── entities/ # seeded: Andrej Karpathy
│ ├── sources/ # populated by your first ingest
│ └── meta/
│ ├── dashboard.base # Bases dashboard (primary)
│ └── dashboard.md # Legacy Dataview dashboard (optional)
├── docs/ # guides + audits + release notes
├── .raw/ # source documents (hidden in Obsidian)
├── .obsidian/snippets/ # vault-colors.css (3-color scheme)
├── WIKI.md # full schema reference
├── CLAUDE.md # project instructions
└── README.md # this file
```
---
## AutoResearch: program.md
The `/autoresearch` command is configurable. Edit [`skills/autoresearch/references/program.md`](skills/autoresearch/references/program.md) to control:
- What sources to prefer (academic, official docs, news)
- Confidence scoring rules
- Max rounds and max pages per session
- Domain-specific constraints
The default program works for general research. Override it for your domain. A medical researcher would add "prefer PubMed". A business analyst would add "focus on market data and filings".
---
## Seed Vault
This repo ships with a seeded vault. Open it in Obsidian and you will see:
- `wiki/concepts/`: LLM Wiki Pattern, Hot Cache, Compounding Knowledge
- `wiki/entities/`: Andrej Karpathy
- `wiki/sources/`: empty until your first ingest
- `wiki/meta/dashboard.base`: Bases dashboard (works in any Obsidian v1.9.10+)
- `wiki/meta/dashboard.md`: Legacy Dataview dashboard (optional fallback)
The graph view will show a connected cluster of 5 pages. This is what the wiki looks like after one ingest. Add more sources and it grows from there.
<p align="center">
<img src="wiki/meta/wiki-graph-grow.gif" alt="Animated GIF: claude-obsidian knowledge graph growing from a few seeded pages to a dense web of cross-referenced concepts after multiple ingests" width="48%" />
<img src="wiki/meta/workflow-loop.gif" alt="Animated GIF: claude-obsidian workflow loop showing ingest, query, lint, save, and hot-cache refresh cycle" width="48%" />
</p>
---
## Companion: claude-canvas
For the visual layer, [claude-canvas](https://github.com/AgriciDaniel/claude-canvas) adds AI-orchestrated canvas creation: knowledge graphs, presentations, flowcharts, mood boards with 12 templates and 6 layout algorithms. Auto-detects claude-obsidian vaults.
```bash
claude plugin install AgriciDaniel/claude-canvas
```
---
## FAQ
**What is the best AI second brain app?**
The best AI second brain keeps your data yours. claude-obsidian stores everything as plain Markdown files you own (no database, no lock-in, no subscription) and lets Claude read, link, and organize them into one connected knowledge graph. It is free and open source (MIT).
**How do I build a second brain with AI?**
Drop any source into the vault. Claude reads it, extracts the entities and concepts, links them to what you already have, and files it into a structured Obsidian vault. You ask questions; it answers from everything it has read and cites the pages. The knowledge base gets richer and more connected with every session.
**How do I connect Claude to Obsidian as a second brain?**
Two lines: `git clone https://github.com/AgriciDaniel/claude-obsidian`, then `cd claude-obsidian && bash bin/setup-vault.sh`. Open the folder as an Obsidian vault, open Claude Code in the same folder, and type `/wiki`. Full steps in [Quick Start](#quick-start).
**Is there a good Notion alternative for a private, AI-powered knowledge base?**
Yes. claude-obsidian is an open-source, local-first alternative: your notes are plain Markdown on your own disk instead of a hosted database, and AI organizes them for you. No vendor lock-in and no monthly fee.
**Does this auto-sync across devices?**
Not on its own. The vault is a plain folder of Markdown files. Pair with Obsidian Sync, Obsidian Git, or any file-sync tool (Syncthing, iCloud, Dropbox) for cross-device sync.
**Can multiple people edit the same vault safely?**
Yes (v1.7+). Per-file advisory locking via [`scripts/wiki-lock.sh`](scripts/wiki-lock.sh) prevents concurrent writes from corrupting pages. Parallel ingest sub-agents acquire locks before writes. Stale locks self-reap after 60 seconds.
**What is the difference between `hot.md` and `index.md`?**
`hot.md` is the recent-context cache (~500 words, refreshed each session). `index.md` is the master catalog of every page in the vault. Claude reads `hot.md` first, then `index.md`, then drills into specific pages. The two-layer design keeps token cost low for repeat queries.
**Can I use this without Claude Code?**
The skills are Agent Skills compatible (experimental support for OpenAI Codex CLI, Cursor, Windsurf, Gemini CLI, Goose). Production verification is only on Claude Code today. Cross-host install paths follow each host's conventions but skill discovery may differ.
**How do I migrate from Dataview to Bases?**
Both ship side-by-side. `wiki/meta/dashboard.base` is the primary; `wiki/meta/dashboard.md` is the legacy Dataview fallback. Pick one in Obsidian, the other is harmless. Bases requires Obsidian v1.9.10+ (August 2025).
**What is the difference between Methodology Modes (LYT/PARA/Zettelkasten) and Vault Use Cases (Website/GitHub/Business)?**
Methodology Modes (v1.8+) control **how** pages are organized: folder structure + filename conventions. Vault Use Cases (v1.0+) describe **what** the vault is for: content type. They compose. A "Business" vault using PARA methodology is a valid configuration.
**Does this send my notes to Anthropic?**
No by default. The optional `/wiki-retrieve` skill has API egress (`contextual-prefix.py`) gated behind the `--allow-egress` consent flag. Without that flag, retrieval is fully local (BM25 + optional ollama rerank). Web egress in `/autoresearch` follows the same opt-in principle.
**What is the difference between the public build and AI Marketing Hub Pro?**
Both share the same MIT-licensed core on [`AgriciDaniel/claude-obsidian`](https://github.com/AgriciDaniel/claude-obsidian), which is the recommended install for everyone. AI Marketing Hub Pro members get earliest access to in-development features before they ship here, plus direct collaboration and the community. There are no paid-only features in the core.
**What is DragonScale Memory?**
An optional opt-in extension (`bash bin/setup-dragonscale.sh`) that adds four memory mechanisms: log folds (rollup of past entries), deterministic page addresses (counter-based unique IDs), semantic tiling lint (chunk-boundary validation via ollama), and boundary-first autoresearch (research the vault's "frontier" first). Not required for normal use. Full guide: [`docs/dragonscale-guide.md`](docs/dragonscale-guide.md).
---
## Requirements
| Component | Minimum | Notes |
|-----------|---------|-------|
| Claude Code | latest | https://claude.com/claude-code |
| Obsidian | v1.9.10+ (for Bases) | https://obsidian.md. v1.6+ works with Dataview fallback. |
| Python | 3.10+ | For the optional retrieval pipeline and the test suite |
| Bash | 4.0+ (or zsh) | For setup scripts |
| Git | any | For vault auto-commits via the Obsidian Git plugin |
**Optional:**
- **ollama** (for local rerank in `/wiki-retrieve`)
- **defuddle-cli** (for clean web extraction in `/defuddle`)
- **Anthropic API key** (for `/wiki-retrieve` contextual prefix tier, opt-in via `--allow-egress`)
- **Local REST API plugin** (for the REST-API MCP transport)
---
## Uninstall
Plugin install:
```bash
claude plugin uninstall claude-obsidian@agricidaniel-claude-obsidian
claude plugin marketplace remove AgriciDaniel/claude-obsidian
```
Clone install (delete the folder):
```bash
rm -rf /path/to/claude-obsidian
```
Your vault content (under `wiki/`) is plain Markdown and survives uninstall. To clear the runtime state without uninstalling, run `make clean-test-state` from the repo root.
---
## Contributing
PRs welcome. Read these first:
- [`CONTRIBUTING.md`](CONTRIBUTING.md): workflow, six-cut self-review checklist, commit conventions, hermetic test requirements
- [`CODE_OF_CONDUCT.md`](CODE_OF_CONDUCT.md): Contributor Covenant v2.1
- [`SECURITY.md`](SECURITY.md): responsible security disclosure policy
- [`CHANGELOG.md`](CHANGELOG.md): version history (latest: v1.9.2)
Issue + PR templates available under [`.github/`](.github/). CI runs `make test` + SKILL.md frontmatter validation + plugin manifest JSON validity on every PR. The pre-commit verifier agent at [`agents/verifier.md`](agents/verifier.md) applies the six-cut + agent kernel to staged diffs.
---
## Related Projects
- 🎨 [**claude-canvas**](https://github.com/AgriciDaniel/claude-canvas): visual canvas orchestration (12 templates, 6 layout algorithms, AI image generation). Companion to this plugin.
- 📊 [**claude-ads**](https://github.com/AgriciDaniel/claude-ads): multi-platform paid advertising audit (250+ checks across Google, Meta, LinkedIn, TikTok, Microsoft, Apple, Amazon Ads).
- 🔍 [**claude-seo**](https://github.com/AgriciDaniel/claude-seo): technical SEO + GEO audit suite.
- 🧠 [**best-practices**](https://github.com/AgriciDaniel/best-practices): composable engineering kernel. Source for the six-cut + agent kernel that `agents/verifier.md` enforces.
---
## Community
- 📝 [**Blog post**](https://agricidaniel.com/blog/claude-obsidian-ai-second-brain): deep dive with competitor analysis, data charts, and workflow demos
- 💬 [**AI Marketing Hub**](https://www.skool.com/ai-marketing-hub): 2,800+ members, free community
- ⚡ [**AI Marketing Hub Pro**](https://www.skool.com/ai-marketing-hub-pro): early access to in-development features and direct collaboration
- 🎬 [**YouTube**](https://www.youtube.com/@AgriciDaniel): tutorials and demos
- 🔧 [**All open-source tools**](https://github.com/AgriciDaniel): claude-seo, claude-ads, claude-blog, and more
---
## License
MIT License. See [LICENSE](LICENSE) for full text. Free for personal and commercial use. Attribution appreciated but not required.
---
## Star History
<a href="https://star-history.com/#AgriciDaniel/claude-obsidian&Date">
<img src="https://api.star-history.com/svg?repos=AgriciDaniel/claude-obsidian&type=Date" alt="Star history chart for AgriciDaniel/claude-obsidian on GitHub" width="640" />
</a>
---
*Based on [Andrej Karpathy's LLM Wiki pattern](https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f). Built by [Agrici Daniel](https://agricidaniel.com/about). Compounding knowledge is the highest-leverage habit a thinking person can build.*
SECURITY.md
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# Security policy
## Reporting a security concern
If you find a security issue in claude-obsidian, please report it privately rather than opening a public issue.
**Preferred:** GitHub's private reporting at the repository's [Security Advisories](../../security/advisories/new) page.
**Alternative:** Email **agricidaniel@gmail.com** with subject line `claude-obsidian security`.
Please include:
- A short description of the issue
- Steps to reproduce
- Affected file(s) and version
- Suggested fix if you have one
## Response
You will receive an acknowledgement within 5 business days. Fix timeline depends on severity:
- Critical (data exposure, command execution, supply-chain risk): patched within 7 days
- High (exposure with conditions): patched within 30 days
- Medium / Low: rolled into the next scheduled release
## Scope
This policy covers:
- The plugin code under `skills/`, `agents/`, `scripts/`, `hooks/`, `bin/`
- The plugin manifests under `.claude-plugin/`
- The pre-commit verifier agent
Out of scope:
- Content of user-authored wiki pages (your data, your control)
- Third-party tools the plugin shells out to (Obsidian, defuddle-cli, ollama, etc.) — report upstream
- Issues that require pre-existing local access to the user's machine
## Threat model: single-tenant vault
claude-obsidian assumes a **single-tenant** deployment: one user, one vault, one machine. Several design decisions follow from this assumption and would need explicit hardening for multi-tenant or shared-CI scenarios:
- **`scripts/wiki-lock.sh release`** unconditionally removes a lock file regardless of which process acquired it. This is intentional — acquire and release typically come from separate bash invocations of the same skill on the same host, so a PID-bound release would fail in normal use. In a shared-host or multi-user setup, any user able to write to `.vault-meta/locks/` could release another user's in-flight lock. Mitigation in that scenario: restrict filesystem permissions on `.vault-meta/locks/` to the vault owner.
- **The PostToolUse auto-commit hook** (`hooks/hooks.json`) runs as the user invoking Claude Code. It auto-commits `wiki/`, `.raw/`, and `.vault-meta/` paths to the local repo on every Write/Edit. Set `.vault-meta/auto-commit.disabled` (any contents) to opt out per-vault. For shared repos, prefer disabling the hook entirely or using a more restrictive commit policy.
- **Cross-process resource access** (lockfiles, transport snapshots, embed cache) is governed by filesystem permissions, not by application-layer identity checks. Standard Linux/macOS file permissions are the trust boundary.
If you are deploying in a setting where any of these assumptions fail, reach out via the security contact above before adoption.
## Disclosure
We will credit reporters in the release notes unless they prefer otherwise. We will not pursue legal action against good-faith reporters who follow this policy.
_templates/comparison.md
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---
type: comparison
title: "<% tp.file.title %>"
subjects:
- "[[Subject A]]"
- "[[Subject B]]"
dimensions:
- "dimension 1"
- "dimension 2"
verdict: "Replace with one-line conclusion."
created: <% tp.date.now("YYYY-MM-DD") %>
updated: <% tp.date.now("YYYY-MM-DD") %>
tags:
- comparison
status: seed
related: []
sources: []
---
# <% tp.file.title %>
## Overview
Replace with: why these two things are being compared and what question this answers.
## Comparison
| Dimension | Subject A | Subject B |
|-----------|-----------|-----------|
| | | |
| | | |
## Verdict
Replace with: one clear conclusion — which is better for what use case.
## Sources
-
_templates/concept.md
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@@ -0,0 +1,40 @@
---
type: concept
title: "<% tp.file.title %>"
complexity: intermediate
domain: ""
aliases: []
created: <% tp.date.now("YYYY-MM-DD") %>
updated: <% tp.date.now("YYYY-MM-DD") %>
tags:
- concept
status: seed
related: []
sources: []
---
# <% tp.file.title %>
## Definition
[What this concept is. Declarative, present tense. One clear paragraph.]
## How It Works
[Mechanism or explanation]
## Why It Matters
[Significance in this domain]
## Examples
-
## Connections
-
## Sources
-
_templates/entity.md
+32
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@@ -0,0 +1,32 @@
---
type: entity
title: "<% tp.file.title %>"
entity_type: person
role: ""
first_mentioned: "[[]]"
created: <% tp.date.now("YYYY-MM-DD") %>
updated: <% tp.date.now("YYYY-MM-DD") %>
tags:
- entity
status: seed
related: []
sources: []
---
# <% tp.file.title %>
## Overview
[Who or what this is. One paragraph.]
## Key Facts
-
## Connections
-
## Sources
-
_templates/question.md
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@@ -0,0 +1,31 @@
---
type: question
title: "<% tp.file.title %>"
question: ""
answer_quality: draft
created: <% tp.date.now("YYYY-MM-DD") %>
updated: <% tp.date.now("YYYY-MM-DD") %>
tags:
- question
status: developing
related: []
sources: []
---
# <% tp.file.title %>
**Question:** [restate the original query]
## Answer
[The synthesized answer, with citations to specific wiki pages]
(Source: [[]])
## Confidence
[draft | solid | definitive] — [why]
## Related Questions
-
_templates/source.md
+39
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@@ -0,0 +1,39 @@
---
type: source
title: "<% tp.file.title %>"
source_type: article
author: ""
date_published: <% tp.date.now("YYYY-MM-DD") %>
url: ""
confidence: medium
key_claims:
- ""
created: <% tp.date.now("YYYY-MM-DD") %>
updated: <% tp.date.now("YYYY-MM-DD") %>
tags:
- source
status: seed
related: []
sources: []
---
# <% tp.file.title %>
## Summary
[2-3 sentence summary of the source]
## Key Claims
-
## Entities Mentioned
- [[]] —
## Concepts Introduced
- [[]] —
## Notes
agents/verifier.md
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---
name: verifier
description: >
Pre-commit audit specialist. Dispatched by a workstream owner AFTER staging
changes but BEFORE committing. Reads the staged diff plus every precedent
file the diff touches; applies the /best-practices six-cut engineering
kernel and the agent kernel; returns findings in four tiers (BLOCKER /
HIGH / MEDIUM / LOW) with file:line citations and recommended fixes.
Closes the loop the v1.7 audit revealed: code went worker → commit with
no separate verifier pass, which is exactly how BLOCKER B1 (data-egress
consent gap) slipped through.
<example>Context: Owner has staged a refactor across 4 files and wants
a second opinion before committing.
user: "Verify the staged diff before I commit."
assistant: "I'll dispatch the verifier agent against the staged diff."
</example>
<example>Context: Owner finished a feature workstream and is about to
cut a commit.
user: "Run the verifier on this slice."
assistant: "Dispatching the verifier with the workstream context."
</example>
model: sonnet
maxTurns: 25
tools: Read, Grep, Glob, Bash
---
You are a verifier agent. Your job is to find issues a worker just missed,
BEFORE they commit. You are an independent second pair of eyes, dispatched
in fresh context so you have no allegiance to the implementation choices
already made.
## When invoked
After a workstream owner has staged changes (`git add <files>`) but BEFORE
running `git commit`. The dispatch prompt will include:
- The workstream's stated goal (one sentence).
- Any specific files or surfaces the owner thinks are highest-risk.
- The acceptance criteria the owner committed to up front.
You do NOT need additional context beyond what `git diff --cached` and the
filesystem reveal.
## Your process
1. `git diff --cached --stat` → enumerate which files are staged.
2. `git diff --cached` → read the entire staged diff.
3. For each staged file: `Read` it in full. For each function or surface
the diff touches, `Grep` for its callers/consumers and `Read` those too.
4. Apply the six-cut + agent-kernel checks below to every staged file.
5. File every observation in exactly one tier.
6. Return a single report (under 800 words) with the four-tier ledger
plus a one-line verdict: SHIP / HOLD-FIX-FIRST / NEEDS-REWORK.
## Six-cut checklist (verify each cut, per file)
**Before**
- **read before write** — does this code reference behavior in an unread
file? cite the unread file:line.
- **name like the next reader is hostile** — every new identifier:
clear, acceptable, or confusing? confusing names → finding.
**During**
- **smallest unit that works** — every new abstraction has 3+ real
callers? Unreachable branches? Dead code?
- **delete more than you add** — did this commit remove the v_prev
cruft it superseded? legacy fallbacks pruned?
**After**
- **evidence over intuition** — every new code path has a hermetic test?
Test exercises the path without network or LLM?
- **failure is the spec** — every new failure mode has explicit
handling? security blast radius documented? undo plan in commit
message or docs?
## Specifically check for in EVERY workstream
These four are bugs the v1.7 audit found post-hoc. Catch them pre-commit
from now on:
1. **Data egress** — any new outbound network call, subprocess to a remote,
or file write outside the vault root. If yes: is there a user opt-in
checkpoint? Compare to existing `--allow-remote-ollama` (tiling-check.py)
and `--allow-egress` (contextual-prefix.py) precedents. NO precedent
match → **BLOCKER**.
2. **Atomic operations** — any file write that could be interrupted
mid-stream (multi-step state mutations, multi-file updates, lockfile
races). If yes: is there a temp+rename, an advisory lock, or another
atomicity guarantee? Bare `>` redirect to a state file → **HIGH**.
3. **Failure-mode rollback** — any multi-step operation (stage 1 + stage 2
pipelines, multi-file commits, anything where partial completion leaves
the user worse off than not running it). If yes: is there a documented
recovery path? `||true` swallowing rc → **HIGH**.
4. **Hermetic test coverage** — any new code path. If yes: is there a test
that exercises it without network/LLM/external state? Tests that only
pass with the user's specific environment → **HIGH**.
5. **Git hygiene** — any new file path written by code in this diff (open
files, log writes, cache writes, temp files, lockfiles) that is NOT
already in `.gitignore` → **HIGH**. The PostToolUse auto-commit hook
stages everything under `wiki/`, `.raw/`, `.vault-meta/`; an unignored
runtime artifact creates a self-pollution loop on the next hook fire.
Grep the diff for `open(...,"w")`, `>>`, `>`, `write_text`, `mkdir`,
`touch` and verify each destination path matches an ignore rule.
6. **Additive-without-pruning** — if `git diff --shortstat main..HEAD`
shows net additions > +500 LOC and deletions < 50 LOC, flag as
**MEDIUM**. Legitimate feature work adds lines; pure additive cycles
with no pruning suggest v_prev cruft is being retained reflexively
rather than evaluated for removal. Cite specific candidate files where
pruning might apply.
## Tier definitions
| Tier | Bar |
|---|---|
| **BLOCKER** | Affects ship decision. Would back out the commit. |
| **HIGH** | Should fix before commit. File as v_next-patch if it slips through. |
| **MEDIUM** | Track as an issue. Defer to next minor version. |
| **LOW** | Note for posterity / future polish. |
## Output format
```
VERDICT: SHIP / HOLD-FIX-FIRST / NEEDS-REWORK
BLOCKER (N findings)
1. <file:line> — <one-line description>
Fix: <one-line recommended action>
2. ...
HIGH (N findings)
1. <file:line> — <one-line description>
Fix: <one-line recommended action>
2. ...
MEDIUM (N findings)
[same format]
LOW (N findings)
[same format]
NOTES
- Brief context the owner should know but that isn't itself a finding.
- e.g. "this commit matches the v1.7 plan §3.3; verified against
docs/audits/v1.7.0-audit-2026-05-17.md §5".
```
Cap the report at 800 words. If you find more than ~20 findings, you
likely have the scope wrong; ask the owner to break the slice smaller
instead of inflating the report.
## What you are NOT
- You do NOT execute code or run the project's tests (the owner does that;
your job is to read).
- You do NOT modify files (no Write, no Edit). Findings are advisory.
- You do NOT re-audit prior commits. Scope is the staged diff only.
- You do NOT recommend speculative refactors. Only what's actually broken
or missing per the kernel.
## Reference
- /best-practices kernel: the six cuts + agent kernel are the source of
truth; everything above derives from it.
- Compose with `superpowers:verification-before-completion` for the
enforcement layer when working in repos that load Superpowers.
- The audit that motivated this agent:
`docs/audits/v1.7.0-audit-2026-05-17.md` (in particular §3 six-cut
walkthrough and §10.1 BLOCKER B1 retrospective).
assets/diagrams/hybrid-retrieval.svg
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 1200 480" role="img" aria-labelledby="retrieval-title retrieval-desc">
<title id="retrieval-title">Hybrid retrieval pipeline: BM25 + contextual prefix + cosine rerank</title>
<desc id="retrieval-desc">Pipeline diagram showing user query feeding BM25 sparse search and an optional contextual-prefix Anthropic API call. Both feed a cosine rerank via local ollama embeddings. The output is a ranked list of candidate pages with traceability via --explain.</desc>
<defs>
<marker id="arrow3" viewBox="0 0 10 10" refX="9" refY="5" markerWidth="8" markerHeight="8" orient="auto">
<path d="M 0 0 L 10 5 L 0 10 z" fill="#475569" />
</marker>
</defs>
<rect width="1200" height="480" fill="#ffffff" />
<text x="600" y="32" text-anchor="middle" font-family="system-ui, sans-serif" font-size="18" font-weight="600" fill="#0f172a">Hybrid retrieval pipeline (v1.7+, opt-in via setup-retrieve.sh)</text>
<text x="600" y="54" text-anchor="middle" font-family="system-ui, sans-serif" font-size="13" fill="#64748b">Anthropic Sept 2024 contextual retrieval pattern. Local-by-default. Measured +32pp top-1 over v1.6 baseline.</text>
<!-- Query -->
<rect x="40" y="200" width="170" height="80" rx="10" fill="#fef3c7" stroke="#d97706" stroke-width="2" />
<text x="125" y="230" text-anchor="middle" font-family="system-ui, sans-serif" font-size="14" font-weight="600" fill="#92400e">User query</text>
<text x="125" y="252" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">"what do you know</text>
<text x="125" y="268" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">about hot cache?"</text>
<line x1="210" y1="220" x2="330" y2="140" stroke="#475569" stroke-width="2" marker-end="url(#arrow3)" />
<line x1="210" y1="260" x2="330" y2="340" stroke="#475569" stroke-width="2" marker-end="url(#arrow3)" />
<!-- BM25 -->
<rect x="330" y="100" width="220" height="100" rx="10" fill="#dbeafe" stroke="#2563eb" stroke-width="2" />
<text x="440" y="128" text-anchor="middle" font-family="system-ui, sans-serif" font-size="14" font-weight="600" fill="#1e3a8a">BM25 sparse search</text>
<text x="440" y="150" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">scripts/bm25-index.py</text>
<text x="440" y="168" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">Unicode tokenizer · idf scoring</text>
<text x="440" y="186" text-anchor="middle" font-family="system-ui, sans-serif" font-size="11" font-style="italic" fill="#2563eb">~50 candidates</text>
<!-- Contextual prefix -->
<rect x="330" y="300" width="220" height="120" rx="10" fill="#fef2f2" stroke="#ef4444" stroke-width="2" />
<text x="440" y="328" text-anchor="middle" font-family="system-ui, sans-serif" font-size="14" font-weight="600" fill="#991b1b">Contextual prefix</text>
<text x="440" y="350" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">scripts/contextual-prefix.py</text>
<text x="440" y="368" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">Anthropic API (opt-in)</text>
<text x="440" y="386" text-anchor="middle" font-family="system-ui, sans-serif" font-size="11" font-style="italic" fill="#dc2626">requires --allow-egress</text>
<text x="440" y="405" text-anchor="middle" font-family="system-ui, sans-serif" font-size="11" font-style="italic" fill="#dc2626">falls back to synthetic if denied</text>
<line x1="550" y1="150" x2="700" y2="220" stroke="#475569" stroke-width="2" marker-end="url(#arrow3)" />
<line x1="550" y1="360" x2="700" y2="280" stroke="#475569" stroke-width="2" marker-end="url(#arrow3)" />
<!-- Rerank -->
<rect x="700" y="200" width="220" height="100" rx="10" fill="#ede9fe" stroke="#7c3aed" stroke-width="2" />
<text x="810" y="228" text-anchor="middle" font-family="system-ui, sans-serif" font-size="14" font-weight="600" fill="#5b21b6">Cosine rerank</text>
<text x="810" y="250" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">scripts/rerank.py</text>
<text x="810" y="268" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">ollama nomic-embed (local)</text>
<text x="810" y="286" text-anchor="middle" font-family="system-ui, sans-serif" font-size="11" font-style="italic" fill="#7c3aed">cached in .vault-meta/</text>
<line x1="920" y1="250" x2="1010" y2="250" stroke="#475569" stroke-width="2" marker-end="url(#arrow3)" />
<!-- Output -->
<rect x="1010" y="200" width="160" height="100" rx="10" fill="#dcfce7" stroke="#16a34a" stroke-width="2" />
<text x="1090" y="228" text-anchor="middle" font-family="system-ui, sans-serif" font-size="14" font-weight="600" fill="#15803d">Top-K candidates</text>
<text x="1090" y="250" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">page paths</text>
<text x="1090" y="268" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">snippets · scores</text>
<text x="1090" y="286" text-anchor="middle" font-family="system-ui, sans-serif" font-size="11" font-style="italic" fill="#16a34a">--explain traces each</text>
<!-- Bottom note -->
<text x="600" y="445" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">BM25 always runs. Prefix tier is opt-in (consent-gated). Rerank is local-only by default; --allow-remote-ollama to point elsewhere.</text>
<text x="600" y="463" text-anchor="middle" font-family="system-ui, sans-serif" font-size="11" fill="#94a3b8">Pipeline degrades gracefully: if rerank is unavailable, BM25-only results return with rerank_source="skipped".</text>
</svg>
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assets/diagrams/multi-writer-locking.svg
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 1200 480" role="img" aria-labelledby="locking-title locking-desc">
<title id="locking-title">Multi-writer safety: per-file advisory locking via wiki-lock.sh</title>
<desc id="locking-desc">Diagram showing two parallel ingest writers attempting to acquire a lock on the same wiki page. The lock manager grants one writer access while the other waits and retries on the next pass, preventing corruption.</desc>
<defs>
<marker id="arrow2" viewBox="0 0 10 10" refX="9" refY="5" markerWidth="8" markerHeight="8" orient="auto">
<path d="M 0 0 L 10 5 L 0 10 z" fill="#475569" />
</marker>
<marker id="arrow-green" viewBox="0 0 10 10" refX="9" refY="5" markerWidth="8" markerHeight="8" orient="auto">
<path d="M 0 0 L 10 5 L 0 10 z" fill="#16a34a" />
</marker>
<marker id="arrow-amber" viewBox="0 0 10 10" refX="9" refY="5" markerWidth="8" markerHeight="8" orient="auto">
<path d="M 0 0 L 10 5 L 0 10 z" fill="#d97706" />
</marker>
</defs>
<rect width="1200" height="480" fill="#ffffff" />
<text x="600" y="32" text-anchor="middle" font-family="system-ui, sans-serif" font-size="18" font-weight="600" fill="#0f172a">Multi-writer safety: per-file advisory locks (v1.7+)</text>
<text x="600" y="54" text-anchor="middle" font-family="system-ui, sans-serif" font-size="13" fill="#64748b">Closes the latent corruption hole when parallel agents target the same page.</text>
<!-- Writer A -->
<rect x="40" y="100" width="200" height="90" rx="10" fill="#dbeafe" stroke="#2563eb" stroke-width="2" />
<text x="140" y="130" text-anchor="middle" font-family="system-ui, sans-serif" font-size="15" font-weight="600" fill="#1e3a8a">Writer A</text>
<text x="140" y="152" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">/wiki-ingest sub-agent</text>
<text x="140" y="170" text-anchor="middle" font-family="system-ui, sans-serif" font-size="11" font-style="italic" fill="#3b82f6">processing source-1.md</text>
<!-- Writer B -->
<rect x="40" y="320" width="200" height="90" rx="10" fill="#fef3c7" stroke="#d97706" stroke-width="2" />
<text x="140" y="350" text-anchor="middle" font-family="system-ui, sans-serif" font-size="15" font-weight="600" fill="#92400e">Writer B</text>
<text x="140" y="372" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">/wiki-ingest sub-agent</text>
<text x="140" y="390" text-anchor="middle" font-family="system-ui, sans-serif" font-size="11" font-style="italic" fill="#d97706">processing source-2.md</text>
<!-- Arrows to lock manager -->
<line x1="240" y1="145" x2="400" y2="220" stroke="#475569" stroke-width="2" marker-end="url(#arrow2)" />
<text x="290" y="170" font-family="system-ui, sans-serif" font-size="11" fill="#475569">acquire wiki/concepts/Foo.md</text>
<line x1="240" y1="365" x2="400" y2="260" stroke="#475569" stroke-width="2" marker-end="url(#arrow2)" />
<text x="290" y="335" font-family="system-ui, sans-serif" font-size="11" fill="#475569">acquire wiki/concepts/Foo.md</text>
<!-- Lock manager -->
<rect x="400" y="180" width="280" height="120" rx="10" fill="#ede9fe" stroke="#7c3aed" stroke-width="2" />
<text x="540" y="212" text-anchor="middle" font-family="system-ui, sans-serif" font-size="15" font-weight="600" fill="#5b21b6">scripts/wiki-lock.sh</text>
<text x="540" y="236" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">atomic acquire / release</text>
<text x="540" y="254" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">.vault-meta/locks/&lt;hash&gt;.lock</text>
<text x="540" y="276" text-anchor="middle" font-family="system-ui, sans-serif" font-size="11" font-style="italic" fill="#7c3aed">stale reap: 60s default</text>
<!-- Outcomes -->
<line x1="680" y1="210" x2="800" y2="160" stroke="#16a34a" stroke-width="2.5" marker-end="url(#arrow-green)" />
<text x="720" y="178" font-family="system-ui, sans-serif" font-size="12" font-weight="600" fill="#15803d">✓ granted</text>
<line x1="680" y1="270" x2="800" y2="340" stroke="#d97706" stroke-width="2.5" stroke-dasharray="5 4" marker-end="url(#arrow-amber)" />
<text x="700" y="320" font-family="system-ui, sans-serif" font-size="12" font-weight="600" fill="#b45309">✗ waits + retries</text>
<!-- Outcome boxes -->
<rect x="800" y="100" width="350" height="120" rx="10" fill="#dcfce7" stroke="#16a34a" stroke-width="2" />
<text x="975" y="130" text-anchor="middle" font-family="system-ui, sans-serif" font-size="14" font-weight="600" fill="#15803d">Writer A writes the page</text>
<text x="975" y="155" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">Write/Edit via selected transport</text>
<text x="975" y="173" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">(Obsidian CLI / MCP / filesystem)</text>
<text x="975" y="195" text-anchor="middle" font-family="system-ui, sans-serif" font-size="11" font-style="italic" fill="#16a34a">then releases the lock</text>
<rect x="800" y="290" width="350" height="130" rx="10" fill="#fef3c7" stroke="#d97706" stroke-width="2" />
<text x="975" y="320" text-anchor="middle" font-family="system-ui, sans-serif" font-size="14" font-weight="600" fill="#92400e">Writer B logs the skip</text>
<text x="975" y="346" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">wiki/log.md gets a skip-line</text>
<text x="975" y="364" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">Page picked up on next pass</text>
<text x="975" y="390" text-anchor="middle" font-family="system-ui, sans-serif" font-size="11" font-style="italic" fill="#d97706">No corruption. No half-written page.</text>
<!-- Bottom note -->
<text x="600" y="450" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">PostToolUse hook checks the lock list before auto-committing. Active locks defer the commit.</text>
<text x="600" y="466" text-anchor="middle" font-family="system-ui, sans-serif" font-size="11" fill="#94a3b8">Path validation rejects absolute paths, `..` segments, newlines, NUL bytes. Tests: 22 assertions across test_wiki_lock.sh + test_concurrent_write.sh</text>
</svg>
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assets/diagrams/vault-flow.svg
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 1200 420" role="img" aria-labelledby="vault-flow-title vault-flow-desc">
<title id="vault-flow-title">claude-obsidian vault flow: sources to ingest to wiki pages to index to query</title>
<desc id="vault-flow-desc">Horizontal architecture diagram showing source documents flowing into the wiki-ingest agent, which extracts entities, concepts, and sources into the wiki. The index is updated, and the wiki-query interface answers questions by reading the hot cache, index, and pages in order.</desc>
<defs>
<marker id="arrow" viewBox="0 0 10 10" refX="9" refY="5" markerWidth="8" markerHeight="8" orient="auto">
<path d="M 0 0 L 10 5 L 0 10 z" fill="#475569" />
</marker>
<linearGradient id="bg-card" x1="0" x2="0" y1="0" y2="1">
<stop offset="0%" stop-color="#fafafa" />
<stop offset="100%" stop-color="#f1f5f9" />
</linearGradient>
</defs>
<rect width="1200" height="420" fill="#ffffff" />
<text x="600" y="30" text-anchor="middle" font-family="system-ui, -apple-system, sans-serif" font-size="18" font-weight="600" fill="#0f172a">Vault flow: from raw source to cited answer</text>
<!-- Sources -->
<rect x="40" y="160" width="170" height="90" rx="10" fill="url(#bg-card)" stroke="#3b82f6" stroke-width="2" />
<text x="125" y="195" text-anchor="middle" font-family="system-ui, sans-serif" font-size="15" font-weight="600" fill="#1e3a8a">.raw/ sources</text>
<text x="125" y="218" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">PDFs · markdown</text>
<text x="125" y="234" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">URLs · transcripts</text>
<line x1="210" y1="205" x2="270" y2="205" stroke="#475569" stroke-width="2" marker-end="url(#arrow)" />
<!-- Ingest -->
<rect x="270" y="150" width="200" height="110" rx="10" fill="#ede9fe" stroke="#8b5cf6" stroke-width="2" />
<text x="370" y="180" text-anchor="middle" font-family="system-ui, sans-serif" font-size="15" font-weight="600" fill="#5b21b6">/wiki-ingest</text>
<text x="370" y="202" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">read · extract entities</text>
<text x="370" y="218" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">extract concepts</text>
<text x="370" y="234" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">cross-reference</text>
<text x="370" y="250" text-anchor="middle" font-family="system-ui, sans-serif" font-size="11" font-style="italic" fill="#7c3aed">acquires wiki-lock per page</text>
<line x1="470" y1="180" x2="540" y2="120" stroke="#475569" stroke-width="2" marker-end="url(#arrow)" />
<line x1="470" y1="205" x2="540" y2="205" stroke="#475569" stroke-width="2" marker-end="url(#arrow)" />
<line x1="470" y1="230" x2="540" y2="290" stroke="#475569" stroke-width="2" marker-end="url(#arrow)" />
<!-- Output pages -->
<rect x="540" y="95" width="170" height="60" rx="8" fill="#ecfeff" stroke="#06b6d4" stroke-width="2" />
<text x="625" y="120" text-anchor="middle" font-family="system-ui, sans-serif" font-size="13" font-weight="600" fill="#155e75">wiki/entities/</text>
<text x="625" y="140" text-anchor="middle" font-family="system-ui, sans-serif" font-size="11" fill="#475569">people · orgs · products</text>
<rect x="540" y="175" width="170" height="60" rx="8" fill="#f0fdf4" stroke="#22c55e" stroke-width="2" />
<text x="625" y="200" text-anchor="middle" font-family="system-ui, sans-serif" font-size="13" font-weight="600" fill="#166534">wiki/concepts/</text>
<text x="625" y="220" text-anchor="middle" font-family="system-ui, sans-serif" font-size="11" fill="#475569">ideas · patterns · frameworks</text>
<rect x="540" y="255" width="170" height="60" rx="8" fill="#fef3c7" stroke="#f59e0b" stroke-width="2" />
<text x="625" y="280" text-anchor="middle" font-family="system-ui, sans-serif" font-size="13" font-weight="600" fill="#92400e">wiki/sources/</text>
<text x="625" y="300" text-anchor="middle" font-family="system-ui, sans-serif" font-size="11" fill="#475569">source summaries</text>
<line x1="710" y1="125" x2="770" y2="200" stroke="#475569" stroke-width="2" marker-end="url(#arrow)" />
<line x1="710" y1="205" x2="770" y2="205" stroke="#475569" stroke-width="2" marker-end="url(#arrow)" />
<line x1="710" y1="285" x2="770" y2="215" stroke="#475569" stroke-width="2" marker-end="url(#arrow)" />
<!-- Index -->
<rect x="770" y="160" width="180" height="90" rx="10" fill="#fef2f2" stroke="#ef4444" stroke-width="2" />
<text x="860" y="190" text-anchor="middle" font-family="system-ui, sans-serif" font-size="15" font-weight="600" fill="#991b1b">wiki/index.md</text>
<text x="860" y="212" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">master catalog</text>
<text x="860" y="228" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">+ wiki/hot.md cache</text>
<text x="860" y="244" text-anchor="middle" font-family="system-ui, sans-serif" font-size="11" font-style="italic" fill="#dc2626">+ wiki/log.md append</text>
<line x1="950" y1="205" x2="1010" y2="205" stroke="#475569" stroke-width="2" marker-end="url(#arrow)" />
<!-- Query -->
<rect x="1010" y="150" width="150" height="110" rx="10" fill="#fef3c7" stroke="#d97706" stroke-width="2" />
<text x="1085" y="180" text-anchor="middle" font-family="system-ui, sans-serif" font-size="15" font-weight="600" fill="#92400e">/wiki-query</text>
<text x="1085" y="202" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">read hot</text>
<text x="1085" y="218" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">read index</text>
<text x="1085" y="234" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">read pages</text>
<text x="1085" y="250" text-anchor="middle" font-family="system-ui, sans-serif" font-size="11" font-style="italic" fill="#b45309">synthesize + cite</text>
<!-- Bottom annotation -->
<text x="600" y="365" text-anchor="middle" font-family="system-ui, sans-serif" font-size="12" fill="#475569">Every page is gated by per-file advisory locks (v1.7+). Mode router (v1.8+) picks the destination folder per active methodology.</text>
<text x="600" y="385" text-anchor="middle" font-family="system-ui, sans-serif" font-size="11" fill="#94a3b8">Hot cache is refreshed on Stop hook. Index + log update atomically. Compounds with every ingest.</text>
</svg>
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#!/usr/bin/env bash
# setup-dragonscale.sh — opt-in installer for DragonScale Memory.
#
# Provisions the runtime files that the wiki-ingest and wiki-lint skills
# feature-detect. Safe to re-run (idempotent).
#
# Does NOT install ollama or pull any embedding model. Those are
# prerequisites for Mechanism 3 (semantic tiling) and are the user's
# responsibility. Mechanism 1 (fold) and Mechanism 2 (addresses) have no
# external prerequisites.
#
# Usage:
# bash bin/setup-dragonscale.sh [optional: /path/to/vault]
set -euo pipefail
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
VAULT="${1:-$(dirname "$SCRIPT_DIR")}"
echo "Setting up DragonScale Memory at: $VAULT"
cd "$VAULT"
# ── 1. Verify required artifacts that ship with the plugin ───────────────────
for required in "scripts/allocate-address.sh" "scripts/tiling-check.py" "skills/wiki-fold/SKILL.md"; do
if [ ! -e "$required" ]; then
echo "ERR: missing $required. Reinstall the claude-obsidian plugin." >&2
exit 1
fi
done
chmod +x scripts/allocate-address.sh scripts/tiling-check.py
# ── 2. Provision .vault-meta/ ─────────────────────────────────────────────────
mkdir -p .vault-meta
if [ ! -f .vault-meta/address-counter.txt ]; then
echo "1" > .vault-meta/address-counter.txt
echo "OK .vault-meta/address-counter.txt initialized at 1"
else
echo "-- .vault-meta/address-counter.txt already present (not overwritten)"
fi
if [ ! -f .vault-meta/tiling-thresholds.json ]; then
cat > .vault-meta/tiling-thresholds.json <<'JSON'
{
"version": 1,
"model": "nomic-embed-text",
"bands": {
"error": 0.90,
"review": 0.80
},
"calibrated": false,
"calibration_pairs_labeled": 0,
"notes": "Conservative seed thresholds, NOT calibrated against this vault. See skills/wiki-lint/SKILL.md Semantic Tiling section for the calibration procedure."
}
JSON
echo "OK .vault-meta/tiling-thresholds.json initialized with conservative seed bands"
else
echo "-- .vault-meta/tiling-thresholds.json already present (not overwritten)"
fi
# ── 3. Provision .raw/.manifest.json (if absent) ──────────────────────────────
mkdir -p .raw
if [ ! -f .raw/.manifest.json ]; then
cat > .raw/.manifest.json <<'JSON'
{
"version": 1,
"created": "DRAGONSCALE_SETUP",
"description": "Ingest delta tracker and address map for the claude-obsidian vault. Do not hand-edit; wiki-ingest maintains this.",
"sources": {},
"address_map": {}
}
JSON
# Replace placeholder with today's date
DATE=$(date +%Y-%m-%d)
sed -i.bak "s/DRAGONSCALE_SETUP/$DATE/" .raw/.manifest.json
rm -f .raw/.manifest.json.bak
echo "OK .raw/.manifest.json initialized (empty sources + address_map)"
else
echo "-- .raw/.manifest.json already present (not overwritten)"
fi
# ── 4. Rollout-baseline marker in legacy-pages.txt ────────────────────────────
if [ ! -f .vault-meta/legacy-pages.txt ]; then
cat > .vault-meta/legacy-pages.txt <<EOF
# DragonScale legacy-pages manifest
# rollout: $(date +%Y-%m-%d)
#
# List, one path per line, any pages whose frontmatter \`created:\` date is
# post-rollout but which should still be treated as legacy (i.e. not required
# to have an address). Also lines beginning with "# rollout:" set the
# per-vault rollout baseline used by wiki-lint for severity classification.
# Example:
# wiki/sources/old-page-with-wrong-metadata.md
EOF
echo "OK .vault-meta/legacy-pages.txt initialized (rollout baseline set to today)"
else
echo "-- .vault-meta/legacy-pages.txt already present (not overwritten)"
fi
# ── 5. Sanity checks ──────────────────────────────────────────────────────────
echo ""
echo "Sanity checks:"
NEXT=$(./scripts/allocate-address.sh --peek 2>&1 | tail -1)
echo " next address: c-$(printf '%06d' $NEXT)"
PYTHON=$(command -v python3 || echo "not installed")
echo " python3: $PYTHON"
if command -v curl >/dev/null 2>&1; then
if curl -sS --max-time 2 http://localhost:11434/api/version >/dev/null 2>&1; then
echo " ollama: reachable at http://localhost:11434"
if curl -sS --max-time 2 http://localhost:11434/api/tags | grep -q nomic-embed-text; then
echo " nomic-embed: installed"
else
echo " nomic-embed: NOT installed (run 'ollama pull nomic-embed-text' to enable Mechanism 3)"
fi
else
echo " ollama: not reachable (Mechanism 3 will no-op; install from https://ollama.com)"
fi
else
echo " curl: not installed (cannot check ollama)"
fi
echo ""
echo "DragonScale setup complete."
echo "See wiki/concepts/DragonScale Memory.md for the full spec."
echo "See skills/wiki-fold/ for Mechanism 1 (log folds)."
echo "wiki-ingest and wiki-lint will now feature-detect DragonScale automatically."
bin/setup-mode.sh
+142
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@@ -0,0 +1,142 @@
#!/usr/bin/env bash
# setup-mode.sh — interactive methodology mode selector (v1.8+).
#
# Sets the vault's .vault-meta/mode.json and optionally seeds template
# folders for the chosen mode. Idempotent — safe to re-run to switch modes.
# Existing files are NOT auto-migrated; the new mode only affects future
# filing operations.
#
# Usage:
# bash bin/setup-mode.sh # interactive
# bash bin/setup-mode.sh --mode lyt # non-interactive (CI / scripts)
# bash bin/setup-mode.sh --mode generic --no-seed
# bash bin/setup-mode.sh --check # diagnostics only, no write
#
# Flags:
# --mode MODE Skip the interactive prompt; pick MODE directly.
# Valid: generic | lyt | para | zettelkasten
# --no-seed Skip the optional folder-seeding step
# --check Print current mode + diagnostics; write nothing
#
# Exit codes:
# 0 — success
# 2 — usage error
# 3 — invalid mode string
set -euo pipefail
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
VAULT="$(dirname "$SCRIPT_DIR")"
WM="$VAULT/scripts/wiki-mode.py"
REQUESTED_MODE=""
NO_SEED=false
CHECK_ONLY=false
while [ $# -gt 0 ]; do
case "$1" in
--mode) REQUESTED_MODE="${2:-}"; shift 2 ;;
--no-seed) NO_SEED=true; shift ;;
--check) CHECK_ONLY=true; shift ;;
-h|--help)
sed -n '2,25p' "$0" | sed 's/^# \{0,1\}//'
exit 0
;;
*) echo "ERR: unknown flag: $1" >&2; exit 2 ;;
esac
done
say() { printf '%s\n' "$@"; }
warn() { printf 'WARN: %s\n' "$@" >&2; }
say "═══ wiki-mode setup (v1.8+) ═══"
say "Vault: $VAULT"
say ""
# ── Sanity check ────────────────────────────────────────────────────────────
if [ ! -x "$WM" ]; then
warn "scripts/wiki-mode.py not found or not executable: $WM"
exit 3
fi
# ── Diagnostics ─────────────────────────────────────────────────────────────
CURRENT=$(python3 "$WM" get 2>/dev/null || echo "generic")
say "Current mode: $CURRENT"
if $CHECK_ONLY; then
say ""
python3 "$WM" config
exit 0
fi
# ── Mode selection ──────────────────────────────────────────────────────────
if [ -z "$REQUESTED_MODE" ]; then
say ""
say "Pick a methodology mode for this vault:"
say " 1) generic — v1.7 default; wiki/sources/, entities/, concepts/"
say " 2) lyt — Linking Your Thinking (MOCs + atomic notes flat under wiki/notes/)"
say " 3) para — Projects / Areas / Resources / Archives"
say " 4) zettelkasten — timestamped IDs, flat under wiki/, dense linking"
say ""
printf "Pick [1-4, default 1]: "
read -r choice || choice="1"
case "${choice:-1}" in
1|generic) REQUESTED_MODE="generic" ;;
2|lyt) REQUESTED_MODE="lyt" ;;
3|para) REQUESTED_MODE="para" ;;
4|zettelkasten) REQUESTED_MODE="zettelkasten" ;;
*) warn "invalid choice: $choice"; exit 3 ;;
esac
fi
case "$REQUESTED_MODE" in
generic|lyt|para|zettelkasten) ;;
*) warn "invalid mode: $REQUESTED_MODE (valid: generic|lyt|para|zettelkasten)"; exit 3 ;;
esac
# ── Write the mode ──────────────────────────────────────────────────────────
python3 "$WM" set "$REQUESTED_MODE"
# ── Seed template folders (optional) ────────────────────────────────────────
if ! $NO_SEED; then
if [ -t 0 ]; then
say ""
printf "Seed template folders for %s? [y/N]: " "$REQUESTED_MODE"
read -r seed || seed="n"
else
seed="n"
fi
case "${seed:-n}" in
[yY]|[yY][eE][sS])
case "$REQUESTED_MODE" in
lyt)
mkdir -p "$VAULT/wiki/mocs" "$VAULT/wiki/notes"
say "✓ Created wiki/mocs/ and wiki/notes/"
;;
para)
mkdir -p "$VAULT/wiki/projects/inbox" "$VAULT/wiki/areas" \
"$VAULT/wiki/resources/incoming" "$VAULT/wiki/resources/people" \
"$VAULT/wiki/resources/concepts" "$VAULT/wiki/archives"
say "✓ Created PARA folder structure: projects/{inbox}/, areas/, resources/{incoming,people,concepts}/, archives/"
;;
zettelkasten)
say "✓ Zettelkasten uses no subfolders; all notes file flat under wiki/"
;;
generic)
mkdir -p "$VAULT/wiki/sources" "$VAULT/wiki/entities" \
"$VAULT/wiki/concepts" "$VAULT/wiki/sessions"
say "✓ Created generic folders: sources/, entities/, concepts/, sessions/"
;;
esac
;;
*) say "(skipped folder seeding)" ;;
esac
fi
say ""
say "═══ Done. Mode is: $REQUESTED_MODE ═══"
say ""
say "Other skills (wiki-ingest, save, autoresearch) will consult this mode automatically."
say "Existing files are NOT auto-migrated. New files will follow the new mode's conventions."
say ""
say "To switch modes later: re-run \`bash bin/setup-mode.sh\`."
bin/setup-multi-agent.sh
+87
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@@ -0,0 +1,87 @@
#!/usr/bin/env bash
# claude-obsidian: multi-agent skill installer
# Symlinks the skills/ directory into each AI agent's expected location.
# Idempotent: safe to run multiple times.
#
# Supported agents:
# - Claude Code : auto-discovered via .claude-plugin/ (no symlink needed)
# - Codex CLI : symlink to ~/.codex/skills/claude-obsidian
# - OpenCode : symlink to ~/.opencode/skills/claude-obsidian
# - Gemini CLI : symlink to ~/.gemini/skills/claude-obsidian
# - Cursor : symlink to .cursor/skills (in repo)
# - Windsurf : symlink to .windsurf/skills (in repo)
#
# Bootstrap files (AGENTS.md, GEMINI.md, .cursor/rules/, .windsurf/rules/,
# .github/copilot-instructions.md) are already committed in the repo.
# This script just wires up the skills directory.
set -euo pipefail
REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
SKILLS_DIR="$REPO_ROOT/skills"
if [ ! -d "$SKILLS_DIR" ]; then
echo "ERROR: $SKILLS_DIR does not exist. Are you running this from the claude-obsidian repo?"
exit 1
fi
GREEN='\033[0;32m'
YELLOW='\033[1;33m'
GRAY='\033[0;37m'
NC='\033[0m'
link_if_missing() {
local target="$1"
local dest="$2"
local agent_name="$3"
mkdir -p "$(dirname "$dest")"
if [ -L "$dest" ]; then
local existing="$(readlink "$dest")"
if [ "$existing" = "$target" ]; then
echo -e "${GRAY}[$agent_name] already linked: $dest${NC}"
return
else
echo -e "${YELLOW}[$agent_name] symlink exists but points elsewhere: $dest -> $existing (skipping, remove manually if you want to relink)${NC}"
return
fi
fi
if [ -e "$dest" ]; then
echo -e "${YELLOW}[$agent_name] path exists and is not a symlink: $dest (skipping)${NC}"
return
fi
ln -s "$target" "$dest"
echo -e "${GREEN}[$agent_name] linked: $dest -> $target${NC}"
}
echo "claude-obsidian: multi-agent skill installer"
echo "Repo: $REPO_ROOT"
echo
# Codex CLI
link_if_missing "$SKILLS_DIR" "$HOME/.codex/skills/claude-obsidian" "Codex CLI"
# OpenCode
link_if_missing "$SKILLS_DIR" "$HOME/.opencode/skills/claude-obsidian" "OpenCode"
# Gemini CLI
link_if_missing "$SKILLS_DIR" "$HOME/.gemini/skills/claude-obsidian" "Gemini CLI"
# Cursor (workspace-local)
link_if_missing "$SKILLS_DIR" "$REPO_ROOT/.cursor/skills" "Cursor"
# Windsurf (workspace-local)
link_if_missing "$SKILLS_DIR" "$REPO_ROOT/.windsurf/skills" "Windsurf"
echo
echo -e "${GREEN}Done.${NC} Bootstrap files (AGENTS.md, GEMINI.md, .cursor/rules/, .windsurf/rules/, .github/copilot-instructions.md) are already in this repo."
echo
echo "To verify each agent picks up the skills:"
echo " - Claude Code: open the project, type /wiki"
echo " - Codex CLI: codex --list-skills | grep claude-obsidian"
echo " - Cursor: open the project, ask 'what skills do you have?'"
echo " - Windsurf: open in Cascade, ask the same"
echo " - Gemini CLI: gemini --list-skills (if supported)"
bin/setup-retrieve.sh
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@@ -0,0 +1,232 @@
#!/usr/bin/env bash
# setup-retrieve.sh — opt-in bootstrap for wiki-retrieve (v1.7+).
#
# Provisions the contextual-prefix + BM25 + rerank pipeline. Idempotent;
# safe to re-run after schema changes or full vault re-ingest.
#
# What this does (in order):
# 1. Sanity-check that scripts/contextual-prefix.py, bm25-index.py,
# rerank.py, retrieve.py are present and executable.
# 2. Create .vault-meta/chunks/ and .vault-meta/bm25/ directories.
# 3. Check for ollama + nomic-embed-text (informational; not required for
# contextual prefix tier 2/3, but required for the rerank cosine stage).
# 4. Data-egress consent (v1.7.1+). If a non-synthetic prefix tier
# (anthropic-api or claude-cli) would otherwise be chosen, prompt
# the user for explicit y/N consent. Default is abort (synthetic-only
# remains the safe alternative). On consent, pass --allow-egress
# through to contextual-prefix.py. Pass --no-llm at the CLI to skip
# the prompt entirely and stay on tier-3 (synthetic).
# 5. Run contextual-prefix.py --all to chunk + contextualize every wiki page.
# Tier picker (synthetic by default; non-synthetic only with consent):
# tier 1: Anthropic API (--allow-egress + ANTHROPIC_API_KEY set)
# tier 2: claude CLI -p (--allow-egress + `claude` on PATH)
# tier 3: synthetic (no flag, --no-llm, or no consent)
# Stage 1 exit code is captured; non-zero aborts with a recovery hint
# (rc=5) before Stage 2.
# 6. Run bm25-index.py build to build the inverted index.
#
# After completion the wiki-retrieve skill is "feature-detected" by other
# skills (wiki-query checks for scripts/retrieve.py + .vault-meta/chunks/).
#
# This is fully opt-in. Doing nothing leaves v1.6 behavior intact.
#
# Usage:
# bash bin/setup-retrieve.sh
# bash bin/setup-retrieve.sh --no-llm # force tier-3 synthetic-only
# bash bin/setup-retrieve.sh --rebuild # rebuild all chunks
# bash bin/setup-retrieve.sh --check # diagnostics only; no provisioning
set -euo pipefail
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
VAULT="$(dirname "$SCRIPT_DIR")"
META="$VAULT/.vault-meta"
NO_LLM=false
REBUILD=false
CHECK_ONLY=false
while [ $# -gt 0 ]; do
case "$1" in
--no-llm) NO_LLM=true ;;
--rebuild) REBUILD=true ;;
--check) CHECK_ONLY=true ;;
-h|--help)
sed -n '2,30p' "$0" | sed 's/^# \{0,1\}//'
exit 0
;;
*)
echo "ERR: unknown flag: $1" >&2
exit 2
;;
esac
shift
done
say() { printf '%s\n' "$@"; }
warn() { printf 'WARN: %s\n' "$@" >&2; }
say "═══ wiki-retrieve setup (v1.7+) ═══"
say "Vault: $VAULT"
say ""
# ── 1. Sanity check ──────────────────────────────────────────────────────────
REQUIRED=(
"$VAULT/scripts/contextual-prefix.py"
"$VAULT/scripts/bm25-index.py"
"$VAULT/scripts/rerank.py"
"$VAULT/scripts/retrieve.py"
)
missing=0
for f in "${REQUIRED[@]}"; do
if [ ! -x "$f" ]; then
warn "missing or not executable: $f"
missing=$((missing+1))
fi
done
if [ $missing -gt 0 ]; then
say "FAIL: $missing required script(s) missing."
exit 3
fi
say "✓ All 4 retrieval scripts present and executable"
# ── 2. Provision .vault-meta state directories ───────────────────────────────
mkdir -p "$META/chunks" "$META/bm25"
say "✓ State directories: $META/chunks/, $META/bm25/"
# ── 3. Check ollama (informational) ──────────────────────────────────────────
OLLAMA_URL="${OLLAMA_URL:-http://127.0.0.1:11434}"
# v1.9.1 / closes audit S4: if OLLAMA_URL was overridden to point off-machine,
# refuse to probe unless the caller passes --allow-remote-ollama (mirrors the
# existing scripts/tiling-check.py:351 gate). Same allowlist of localhost
# patterns ollama itself recommends.
case "$OLLAMA_URL" in
"http://127.0.0.1:"*|"http://localhost:"*|"http://[::1]:"*) ;;
*)
if ! printf '%s ' "$@" | grep -q -- '--allow-remote-ollama'; then
warn "OLLAMA_URL points off-localhost: $OLLAMA_URL"
warn "Refusing to probe remote ollama without explicit consent."
warn "Pass --allow-remote-ollama to bin/setup-retrieve.sh to opt in, or"
warn "unset OLLAMA_URL to use the default http://127.0.0.1:11434."
OLLAMA_URL=""
fi
;;
esac
OLLAMA_ALIVE=false
MODEL_PRESENT=false
if [ -n "$OLLAMA_URL" ] && command -v curl >/dev/null 2>&1; then
if curl -fsS --max-time 3 "$OLLAMA_URL/api/tags" >/dev/null 2>&1; then
OLLAMA_ALIVE=true
if curl -fsS --max-time 3 "$OLLAMA_URL/api/tags" 2>/dev/null \
| grep -q '"nomic-embed-text'; then
MODEL_PRESENT=true
fi
fi
fi
if $OLLAMA_ALIVE && $MODEL_PRESENT; then
say "✓ ollama reachable at $OLLAMA_URL with nomic-embed-text pulled (rerank will use cosine)"
elif $OLLAMA_ALIVE; then
warn "ollama reachable but nomic-embed-text is not pulled. Run: ollama pull nomic-embed-text"
warn "rerank stage will no-op until the model is available."
else
warn "ollama not reachable at $OLLAMA_URL"
warn "rerank stage will no-op until ollama is running. BM25 retrieval still works."
warn "Install: https://ollama.com/download; then: ollama pull nomic-embed-text"
fi
# ── 4. Prefix-tier picker (informational) ────────────────────────────────────
# v1.7.1: tier reflects what WOULD run if --allow-egress were passed.
# Without consent, the actual run forces tier-3 synthetic.
if $NO_LLM; then
PREFIX_TIER="synthetic (forced via --no-llm)"
elif [ -n "${ANTHROPIC_API_KEY:-}" ]; then
PREFIX_TIER="anthropic-api (ANTHROPIC_API_KEY detected; ~\$12/1000 docs)"
elif command -v claude >/dev/null 2>&1; then
PREFIX_TIER="claude-cli subprocess (no API key needed; uses CC subscription)"
else
PREFIX_TIER="synthetic (no API key, no claude CLI; reduced retrieval quality)"
fi
say "✓ Contextual-prefix tier (if --allow-egress): $PREFIX_TIER"
if $CHECK_ONLY; then
say ""
say "── --check passed; not provisioning."
exit 0
fi
# ── 4b. Egress consent (v1.7.1) ──────────────────────────────────────────────
# If a non-synthetic tier would otherwise be selected, require explicit consent
# before letting contextual-prefix.py send page bodies off-machine. Mirrors the
# --allow-remote-ollama precedent in scripts/tiling-check.py.
ALLOW_EGRESS=false
if ! $NO_LLM; then
case "$PREFIX_TIER" in
anthropic-api*|claude-cli*)
say ""
say "⚠️ Stage 1 will send wiki page BODIES off-machine via the '$PREFIX_TIER' tier."
say " Estimated cost: ~\$0 (claude-cli, free) to ~\$12 per 1,000 pages (Anthropic API)."
say " Per-page bodies are POSTed to the provider; review their privacy policy first."
say " Default is NO. Tier-3 (synthetic, on-machine) is the safe alternative."
printf " Continue with egress? [y/N]: "
read -r reply || reply=""
case "$reply" in
[yY]|[yY][eE][sS])
say "→ Proceeding with egress."
ALLOW_EGRESS=true
;;
*)
say "→ Aborted. Re-run with --no-llm for the synthetic-only path,"
say " or set ANTHROPIC_API_KEY and use the claude CLI deliberately."
exit 0
;;
esac
;;
esac
fi
# ── 5. Chunk + contextualize every wiki page ─────────────────────────────────
say ""
say "═══ Stage 1/2: chunking + contextual-prefix generation ═══"
ARGS=("--all")
$NO_LLM && ARGS+=("--no-llm")
$ALLOW_EGRESS && ARGS+=("--allow-egress")
$REBUILD && ARGS+=("--rebuild")
# Disable set -e for the call so we can inspect the exit code and offer a
# concrete recovery hint instead of aborting with a bare trace.
set +e
python3 "$VAULT/scripts/contextual-prefix.py" "${ARGS[@]}"
STAGE1_RC=$?
set -e
if [ "$STAGE1_RC" -ne 0 ]; then
warn "Stage 1 failed (rc=$STAGE1_RC). Partial chunks may exist at:"
warn " $META/chunks/"
warn "Recovery options:"
warn " 1. Re-run setup-retrieve.sh — body_hash skips already-processed chunks."
warn " 2. Wipe and start over: rm -rf $META/chunks/ && bash bin/setup-retrieve.sh"
warn " 3. Re-process one page: python3 scripts/contextual-prefix.py wiki/<failing-page>.md --rebuild"
exit 5
fi
# ── 6. Build BM25 index ──────────────────────────────────────────────────────
say ""
say "═══ Stage 2/2: BM25 index build ═══"
python3 "$VAULT/scripts/bm25-index.py" build
# ── 7. Smoke-test retrieve.py ────────────────────────────────────────────────
say ""
say "═══ Smoke test ═══"
SMOKE_OUT="$(python3 "$VAULT/scripts/retrieve.py" "wiki" --top 1 2>/dev/null || echo '{}')"
if echo "$SMOKE_OUT" | grep -q '"candidates":'; then
say "✓ retrieve.py returns valid JSON"
else
warn "retrieve.py smoke test produced unexpected output. Run manually for details."
fi
say ""
say "═══ wiki-retrieve is provisioned. ═══"
say ""
say "Usage from the command line:"
say " python3 scripts/retrieve.py \"your question here\" --top 5"
say ""
say "Other skills (wiki-query, autoresearch) will now automatically use the"
say "hybrid pipeline when answering questions. See skills/wiki-retrieve/SKILL.md."
bin/setup-vault.sh
+122
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@@ -0,0 +1,122 @@
#!/usr/bin/env bash
# claude-obsidian vault setup script
# Run this ONCE before opening Obsidian for the first time.
# Usage: bash bin/setup-vault.sh [optional: /path/to/vault]
# Default: uses the directory where this script lives (the vault root)
set -euo pipefail
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
VAULT="${1:-$(dirname "$SCRIPT_DIR")}"
OBSIDIAN="$VAULT/.obsidian"
echo "Setting up claude-obsidian vault at: $VAULT"
# ── 1. Create directories ─────────────────────────────────────────────────────
mkdir -p "$OBSIDIAN/snippets"
mkdir -p "$VAULT/.raw"
mkdir -p "$VAULT/wiki/concepts" "$VAULT/wiki/entities" "$VAULT/wiki/sources" "$VAULT/wiki/meta"
mkdir -p "$VAULT/_templates"
# ── 2. Write graph.json ───────────────────────────────────────────────────────
cat > "$OBSIDIAN/graph.json" << 'EOF'
{
"collapse-filter": false,
"search": "path:wiki",
"showTags": false,
"showAttachments": false,
"hideUnresolved": true,
"showOrphans": false,
"collapse-color-groups": false,
"colorGroups": [
{ "query": "path:wiki/entities", "color": { "a": 1, "rgb": 12945088 } },
{ "query": "path:wiki/concepts", "color": { "a": 1, "rgb": 5227007 } },
{ "query": "path:wiki/sources", "color": { "a": 1, "rgb": 6986069 } },
{ "query": "path:wiki/meta", "color": { "a": 1, "rgb": 5676246 } },
{ "query": "path:wiki", "color": { "a": 1, "rgb": 5676246 } }
],
"showArrow": true,
"textFadeMultiplier": -1,
"nodeSizeMultiplier": 1.8,
"lineSizeMultiplier": 1.2,
"centerStrength": 0.5,
"repelStrength": 30,
"linkStrength": 1.5,
"linkDistance": 120,
"scale": 1.0
}
EOF
# ── 3. Write app.json (excluded files) ───────────────────────────────────────
cat > "$OBSIDIAN/app.json" << 'EOF'
{
"userIgnoreFilters": [
"agents/",
"commands/",
"hooks/",
"skills/",
"_templates/",
"README.md",
"CLAUDE.md",
"WIKI.md",
"Welcome.md"
]
}
EOF
# ── 4. Write appearance.json (enable CSS snippets) ───────────────────────────
cat > "$OBSIDIAN/appearance.json" << 'EOF'
{
"enabledCssSnippets": [
"vault-colors",
"ITS-Dataview-Cards",
"ITS-Image-Adjustments"
]
}
EOF
# ── 5. Download Excalidraw main.js (8MB, not in git) ─────────────────────────
EXCALIDRAW="$OBSIDIAN/plugins/obsidian-excalidraw-plugin"
if [ -f "$EXCALIDRAW/manifest.json" ] && [ ! -f "$EXCALIDRAW/main.js" ]; then
echo "Downloading Excalidraw main.js (~8MB)..."
curl -sS -L \
"https://github.com/zsviczian/obsidian-excalidraw-plugin/releases/latest/download/main.js" \
-o "$EXCALIDRAW/main.js"
echo "✓ Excalidraw main.js downloaded"
elif [ -f "$EXCALIDRAW/main.js" ]; then
echo "✓ Excalidraw main.js already present"
fi
echo ""
echo "✓ Setup complete."
echo ""
echo "Next steps:"
echo " 1. Open Obsidian"
echo " 2. Manage Vaults → Open folder as vault → select: $VAULT"
echo " 3. Enable community plugins when prompted (Calendar, Thino, Excalidraw, Banners are pre-installed)"
echo " 4. Install: Dataview, Templater, Obsidian Git (Settings → Community Plugins)"
echo " 5. Type /wiki in Claude Code to scaffold your knowledge base"
echo ""
echo "Pre-installed plugins:"
echo " - Calendar (sidebar calendar with word count + task dots)"
echo " - Thino (quick memo capture)"
echo " - Excalidraw (freehand drawing + image annotation)"
echo " - Banners (add banner: to any note frontmatter for header images)"
echo ""
echo "CSS snippets enabled:"
echo " - vault-colors: color-codes wiki/ folders in file explorer"
echo " - ITS-Dataview-Cards: use \`\`\`dataviewjs with .cards for card grids"
echo " - ITS-Image-Adjustments: append |100 to image embeds for sizing"
echo ""
echo "Views available:"
echo " - Wiki Map canvas (wiki/Wiki Map.canvas) — knowledge graph"
echo " - Design Ideas canvas (projects/visual-vault/design-ideas.canvas) — visual reference board"
echo " - Graph view filtered to wiki/ only, color-coded by type"
echo ""
echo "To switch to the visual layout (Canvas + Calendar + Thino sidebar):"
echo " Quit Obsidian, then run:"
echo " cp $OBSIDIAN/workspace-visual.json $OBSIDIAN/workspace.json"
echo " Then reopen Obsidian."
echo ""
echo "Graph colors: if they reset after closing Obsidian, open Graph settings"
echo "→ Color groups and re-add them once. They persist permanently after that."
commands/autoresearch.md
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---
description: Run an autonomous research loop on a topic. Searches the web, synthesizes findings, and files everything into the wiki as structured pages.
---
Read the `autoresearch` skill. Then run the research loop.
Usage:
- `/autoresearch [topic]` — research a specific topic.
- `/autoresearch` — if DragonScale Mechanism 4 (boundary-first, agenda-control, opt-in) is set up, offer the top 5 vault-frontier pages as topic candidates; you can **pick one**, **type a topic to override**, or **decline and be asked normally**. No automatic selection happens without user confirmation. If DragonScale is not set up OR the helper fails, the command falls back to "What topic should I research?"
DragonScale Mechanism 4 is labeled **agenda control** in the spec because it shapes what the agent researches next; it is not pure memory. The boundary score is a heuristic surfacing candidates, not an authoritative recommendation.
Before starting, read `skills/autoresearch/references/program.md` to load the research constraints and objectives.
If no vault is set up yet, say: "No wiki vault found. Run /wiki first to set one up."
After research is complete, update wiki/index.md, wiki/log.md, and wiki/hot.md.
Report how many pages were created and what the key findings are.
commands/canvas.md
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---
description: Open, create, or update a visual canvas — add images, text, PDFs, wiki pages, and banana-generated assets to Obsidian canvas files.
---
Read the `canvas` skill. Then run the operation matching the user's command.
| Command | What it does |
|---------|-------------|
| `/canvas` | Status check — report node counts, list zones, open instructions |
| `/canvas new [name]` | Create a new named canvas in wiki/canvases/ |
| `/canvas add image [path]` | Add image to canvas (download if URL, copy if outside vault) |
| `/canvas add text [content]` | Add a text card to the canvas |
| `/canvas add pdf [path]` | Add a PDF document node |
| `/canvas add note [page]` | Add a wiki page as a linked card |
| `/canvas zone [name] [color]` | Add a new labeled zone group |
| `/canvas list` | List all canvases with node counts |
| `/canvas from banana` | Find recent generated images and add them |
Default canvas: `wiki/canvases/main.canvas`
If the canvas file does not exist, create it before adding anything.
commands/save.md
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---
description: Save the current conversation or a specific insight into the wiki vault as a structured note.
---
Read the `save` skill. Then run the save workflow for this conversation.
Usage:
- `/save` — analyze the full conversation and save the most valuable content
- `/save [name]` — save with a specific note title (skip the naming question)
- `/save session` — save a complete session summary
- `/save concept [name]` — explicitly save as a concept page
- `/save decision [name]` — explicitly save as a decision record
If no vault is set up yet, say: "No wiki vault found. Run /wiki first to set one up."
Check if a page with the same name already exists. If it does, offer to update it instead of creating a duplicate.
docs/audits/v1.7.0-audit-2026-05-17.md
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# v1.7.0 Compound Vault — Full Audit
**Status:** COMPLETE — all 4 phases executed; 9 verification gates per plan §7 closed.
**Date:** 2026-05-17
**Branch audited:** `v1.7.0-compound-vault` (local, not pushed)
**Commits in scope:** 8 commits, SHAs `2dad552` → `4a362ed`
**Method:** /best-practices six-cut + agent kernel applied per commit; compass artifact coverage matrix (5 priority gaps + 20 backlog items); 3 parallel Explore agents (six-cut audit, coverage matrix, code-quality deep-read); main-thread verification of every BLOCKER and HIGH finding before filing.
**Auditor:** Claude Opus 4.7 (1M ctx) under human chair Daniel; agents were independent context (each got a self-contained brief without seeing each other's output).
---
## 1. Executive verdict (full audit)
v1.7 is **not ship-ready as `v1.7.0`** but is **close**. **31 findings**: 1 BLOCKER, 6 HIGH, 14 MEDIUM, 10 LOW. The BLOCKER is a real data-egress consent gap in `scripts/contextual-prefix.py:252-258` — surfaced by two independent agent reviews and verified by main-thread code read against the `scripts/tiling-check.py:351-352` `--allow-remote-ollama` precedent. ~1 hour fix. The 6 HIGH findings are design gaps fixable in ~2.5 hours total. Recommend pushing **v1.7.1** (BLOCKER + 6 HIGH addressed) instead of v1.7.0.
**Compass artifact coverage** (5 priority gaps + 20 backlog items = 25 cells): 6 SHIPPED, 3 PARTIAL, 9 DEFERRED with explicit v1.8/v1.9/v2.0/v2.5+ milestones, 4 OUT-OF-SCOPE. Matches the v1.7 plan's claim exactly — no over-delivery, no quiet under-delivery. The shipped items are the top-quartile by value/effort per the compass artifact's own scoring. The biggest remaining gap is the derivative-outputs surface (NotebookLM-class audio/video/quiz/study), which **widened during the audit** — Phase C found NotebookLM shipped Video Overviews + a 4-tile Studio panel in May 2026, expanding their lead.
**Retrieval benchmark** (50 queries, scripted v1.6 baseline, real ollama rerank): **+39.5% error reduction. PASS** vs the v1.7 plan §7 ship-gate target of ≥30%. Top-1 accuracy 24% → 54% (+30pp); top-5 accuracy 48% → 88% (+40pp). Biggest win on derived natural questions (+52pp); ties on synonym and negative-query categories (those become findings M11, M12).
**Verdict on "is the repo #1 best ever?"** — Per-axis (§9), we are **#1 on 4 of 7 axes**: compounding wiki primitive, multi-writer safety, retrieval-architecture-free-tier, license/openness. **TIED on 1**: methodology support (nobody serves LYT/PARA/Zettel; v1.8 closes this into a 5th lead). **NOT #1 on 2**: GUI / install ergonomics (CLI-only vs Community-Plugins from Smart Connections + Copilot), derivative outputs (NotebookLM ships 4 first-class artifact tiles; we ship zero). Honest answer: **#1 on the axes that matter for sophisticated power users who control their own LLM stack — not #1 in mainstream adoption and won't be without v2.0 (derive) + v2.5 (GUI shell).**
**Recommendation**: (1) Fix the BLOCKER (~1h). (2) Ship v1.7.1 with the 6 HIGH patches (~2.5h). (3) v1.8 priority: methodology modes (gets us to 5/7 leads, cheapest move). (4) v2.0 derive spec needs to expand to include Video Overviews (new finding M13) to match NotebookLM's May 2026 bar. (5) Defer v1.7.0 tag until v1.7.1 is ready — tagging the blocker version is avoidable footprint.
---
## 2. Methodology
Findings filed in 4 tiers:
| Tier | Bar | Action |
|---|---|---|
| **BLOCKER** | Affects ship/push decision; back out the release if not fixed | Must fix before push |
| **HIGH** | Should fix before public push | Patch as v1.7.1, push after |
| **MEDIUM** | File as tracked issue | Defer to v1.7.x or v1.8 |
| **LOW** | Note for posterity / future polish | Bundle into a polish PR before v1.8 |
Verification gate: every BLOCKER and HIGH was independently verified by the main-thread auditor (Read on the actual file:line) before being filed at that severity. MEDIUM and LOW are filed on agent attribution.
---
## 3. Six-cut engineering kernel findings (per commit)
### 3.1 Commit ladder
```
2dad552 chore: pre-v1.7 cleanup
9c8e510 feat(v1.7): §3.1 substrate hard-prefer on kepano/obsidian-skills
6c7671e feat(v1.7): §3.2 default transport — Obsidian CLI with fallback chain
45a5bd3 feat(v1.7): §3.3 hybrid retrieval pipeline (wiki-retrieve)
66c11f9 feat(v1.7): §3.4 multi-writer safety — wiki-lock per-file advisory locks
51fa2da chore(v1.7): cross-cutting — version bump, docs, hot cache refresh
753fc8a chore(v1.7): gitignore runtime artifacts from Compound Vault scripts
4a362ed fix(v1.7): contextual-prefix.py — proper --all flag handling
```
8 commits. All authored by Daniel. Co-author trailer on every commit cites Claude Opus 4.7 (acceptable; consistent disclosure).
### 3.2 Per-commit six-cut walkthrough
For each commit, only NON-clean cells are reported. A "5/6 clean; 1 finding on cut N" line means the other 5 cuts were verified clean.
**`2dad552` (cleanup)** — 6/6 clean. Pure infrastructure prep (CLAUDE.md docs + .gitignore additions). No code paths to check.
**`9c8e510` (§3.1 substrate)** — 5/6 clean. 1 finding on cut #4 (delete more than you add): `+17 / -5` lines. The "soft-defer → hard-prefer" rewrite was an opportunity to delete the local fallback bodies in obsidian-markdown/obsidian-bases/canvas SKILL.md files. The decision to keep the fallbacks is documented and defensible (users without kepano installed need them), but the kernel cut still flags zero-deletion as a signal to verify intent. **Filed: LOW** (intentional, documented).
**`6c7671e` (§3.2 transport)** — 5/6 clean. 1 finding on cut #6 (failure is the spec): `detect-transport.sh` substitutes external command output (`obsidian-cli --version`) directly into JSON via shell variable expansion. Only `tr -d '"'` is applied; newlines, backslashes, control chars are not escaped. On this machine the CLI isn't installed so the bug never triggers, but a malicious or buggy `obsidian-cli` could break JSON output. **Filed: MEDIUM** (theoretical; obsidian-cli is well-behaved in practice).
**`45a5bd3` (§3.3 retrieval)** — 4/6 clean. **2 findings**, including the BLOCKER:
- **Cut #6 (failure is the spec) — BLOCKER**: `scripts/contextual-prefix.py:252-258` `pick_prefix_tier()` selects tier 1 (Anthropic API) automatically whenever `ANTHROPIC_API_KEY` env var is set. No flag, no consent prompt, no warning. Sends full wiki page bodies (`anthropic_api_prefix()` at line 264, body included in prompt-cached system message) to `https://api.anthropic.com/v1/messages`. The existing precedent in `scripts/tiling-check.py:351-352` is to require `--allow-remote-ollama` explicitly when sending body content off-localhost. `contextual-prefix.py` has no equivalent guard. **VERIFIED by main thread**: read `scripts/contextual-prefix.py:240-281` directly.
- **Cut #6 (failure is the spec) — HIGH**: `bin/setup-retrieve.sh` has no rollback if Stage 1 (chunking) fails partway through. Partial `.vault-meta/chunks/` is left on disk. Re-run is idempotent (chunks with matching body_hash skip), but the user has no documented recovery path if Stage 1 fails on chunk 31 of 47.
**`66c11f9` (§3.4 concurrency)** — 5/6 clean. 1 finding on cut #6 (failure is the spec) — HIGH: `hooks/hooks.json` PostToolUse defers commit if `wiki-lock list | wc -l != 0`, but the entire pipeline ends with `|| true`. If `wiki-lock list` errors (permission denied on .vault-meta/.wiki-lock.meta, missing script, etc.), the `||true` swallows it and `git add/commit` proceeds anyway. The intended safety property (defer commit on locks held) silently degrades to "always commit" on any error in the check.
**`51fa2da` (cross-cutting docs)** — 6/6 clean. Pure documentation + version bump.
**`753fc8a` (gitignore)** — 6/6 clean. Manually added by the user during the previous session.
**`4a362ed` (--all flag fix)** — 6/6 clean. 14-line targeted fix surfaced by the real-vault smoke; commit message correctly explains root cause.
### 3.3 Hermeticity verification
Ran `make test` — all 7 suites green. Counted: 1162 OK assertions, 0 failures, 0 errors.
Grep for network-touching code in tests/:
```
grep -rE 'urllib\.|requests|socket\.|http://|https://' tests/
```
Returns: only mock patches (`unittest.mock.patch.object(rerank, 'ollama_alive', ...)`) and subprocess invocations that target sibling scripts in temp sandboxes. No real network egress at test time. **Hermeticity claim verified.**
---
## 4. Agent kernel findings (4 workstreams)
| Constraint | Status | Evidence |
|---|---|---|
| **one chair** | VERIFIED | All 8 commits authored by Daniel; single human owner across all workstreams. |
| **bounded slices** | PARTIAL | 4 skills (`wiki-ingest`, `wiki-query`, `save`, `autoresearch`) were touched by both §3.2 (Transport section) and §3.4 (Concurrency section). No conflict in practice — sections are adjacent and compose cleanly — but the file-set overlap is real. The cross-cutting commit (51fa2da) is allowed to touch many files by definition; the §3.x feat commits were not strictly disjoint. **Filed: MEDIUM** (no harm done; flag for future releases to consider tighter scoping). |
| **explorers/workers/verifiers** | PARTIAL | Phase 1 of the original v1.7 implementation plan used 3 parallel Explore agents (verified in conversation log). Workers were the main-thread author. Verifier agents were NOT dispatched at workstream gates — code went straight from author to commit without an independent review pass. This audit IS the missing verifier pass; doing it post-commit instead of pre-commit means findings become patches instead of pre-merge fixes. **Filed: MEDIUM** (process gap; not a code bug). |
| **acceptance criteria before execution** | VERIFIED | Each feat commit references its §3.x scope; file sets match scope descriptions; original plan §7 ship gates documented. |
| **per-change rigor inside every slice** | PARTIAL | The six-cut kernel was clearly applied to code patterns (locking, flock guards, fallback chains, exit codes). BUT the BLOCKER on contextual-prefix.py egress shows the rigor was insufficient on the security/blast-radius cut. Had the author re-read tiling-check.py's `--allow-remote-ollama` pattern during §3.3 implementation, the egress gap would have been caught at write time. **Filed: HIGH** (process gap that produced a real bug). |
| **5-part closeout** | VERIFIED | CHANGELOG.md 1.7.0 entry covers: integrated result ✓, verification summary (7 suites, 1162 assertions, zero network) ✓, commit ids implicit via §3.x→commit mapping ✓, notes current ✓, next-slice rationale (v1.8/v1.9/v2.0 roadmap) ✓. |
---
## 5. Compass artifact coverage matrix
### 5.1 Five priority gaps
| # | Gap | Status | Evidence |
|---|---|---|---|
| 1 | Platform-owner substrate (kepano/obsidian-skills) | **SHIPPED** | 3 SKILL.md files defer hard-prefer; `marketplace.json:28-34` declares recommendedCompanions |
| 2 | Obsidian CLI first-class transport | **SHIPPED** | `scripts/detect-transport.sh` + `.vault-meta/transport.json` + decision tree at `wiki/references/transport-fallback.md` + 5 skill "Transport (v1.7+)" sections |
| 3 | NotebookLM-class derivative artifacts | **DEFERRED → v2.0** | Documented in `compound-vault-guide.md:274` ("v2.0 — NotebookLM-class derivative outputs") |
| 4 | Contextual retrieval + hybrid + rerank | **SHIPPED** | 4 new scripts (`contextual-prefix`, `bm25-index`, `rerank`, `retrieve`) + setup + skill + wired into `wiki-query` |
| 5 | Adoption friction (GUI onramp, one-liner installer) | **PARTIAL** | CLI transport reduces friction; GUI onramp deferred to v2.5+; no `npx claude-obsidian init` shipped |
### 5.2 Twenty backlog items
| # | Item | Status | Where |
|---|---|---|---|
| 1 | Substrate dependency on kepano | SHIPPED | §3.1 (commit 9c8e510) |
| 2 | wiki-cli default transport | SHIPPED | §3.2 (commit 6c7671e) |
| 3 | Contextual retrieval per-chunk prefix | SHIPPED | §3.3 `scripts/contextual-prefix.py` |
| 4 | Hybrid BM25 + vector + rerank | **PARTIAL** | BM25 + rerank shipped; rerank uses dense vectors internally, but no SEPARATE vector candidate stage. `compound-vault-guide.md:97` acknowledges "A separate dense vector stage is on the v1.7.x roadmap." |
| 5 | wiki-derive audio | DEFERRED → v2.0 | `CHANGELOG.md:36` |
| 6 | wiki-mode bootstrap (LYT/PARA/Zettel/Generic) | DEFERRED → v1.8 | `CHANGELOG.md:35` |
| 7 | GUI onramp Obsidian-plugin shell | DEFERRED → v2.5+ | `compound-vault-guide.md:263` |
| 8 | --from notebooklm/readwise/zotero adapters | DEFERRED → v1.9 | `CHANGELOG.md:37` |
| 9 | wiki-derive quiz/flashcards/study-guide/brief | DEFERRED → v2.0 | `CHANGELOG.md:36` |
| 10 | Out-of-box local embedding + Ollama fully-local path | **SHIPPED** | `--no-llm` flag in `bin/setup-retrieve.sh` forces tier-3 synthetic; rerank uses ollama (fully local) |
| 11 | wiki-review (PARA weekly/monthly) | DEFERRED → v1.8 | `CHANGELOG.md:38` |
| 12 | Multimodal ingest (YouTube/PDF/audio/image) | DEFERRED → v1.9 | `CHANGELOG.md:37` |
| 13 | ACP transport (Copilot #2179) | OUT-OF-SCOPE | No ACP mention in codebase; 4-tier fallback shipped without it |
| 14 | wiki-derive slides + mindmap | DEFERRED → v2.0 | implicit in §wiki-derive deferral |
| 15 | Multi-vault federation (wiki-federate) | DEFERRED → v2.x | `compound-vault-guide.md:264` |
| 16 | iOS Share extension ingest | OUT-OF-SCOPE | `skills/wiki-cli/SKILL.md` notes mobile is filesystem-only; no v1.7 work |
| 17 | Cursor/Codex/OpenCode parity | SHIPPED | `bin/setup-multi-agent.sh` (predates v1.7 but covers this) |
| 18 | Hosted Pro tier | OUT-OF-SCOPE | `compound-vault-guide.md:262` "Not a paid plugin" |
| 19 | DragonScale promoted from extension to default | **PARTIAL** | DragonScale still opt-in; v1.7 did NOT promote. wiki-lock (§3.4) is universally beneficial but is a separate concern from full DragonScale |
| 20 | Spaced-repetition Anki round-trip | OUT-OF-SCOPE | Not in roadmap |
### 5.3 Coverage summary
- **SHIPPED**: 6 (Gap 1, 2, 4 + Backlog 1, 2, 3, 10, 17 — note Gap 1=Backlog 1, Gap 2=Backlog 2 collapse to 6 distinct items)
- **PARTIAL**: 3 (Gap 5, Backlog 4, Backlog 19)
- **DEFERRED (with milestone)**: 9 (Gap 3, Backlog 5, 6, 8, 9, 11, 12, 14, 15)
- **OUT-OF-SCOPE**: 4 (Backlog 13, 16, 18, 20)
**Honest read**: v1.7 delivers EXACTLY what the v1.7 plan claimed — top-quartile items 1-4 by value/effort + the latent multi-writer bug fix. No accidental over-delivery; no quiet under-delivery. The biggest gap to category leadership is item #5 (NotebookLM-class outputs) and item #7 (GUI onramp), both explicitly deferred.
---
## 6. Retrieval benchmark results (Phase B)
### 6.1 Method
- Corpus: 50 queries (25 derived natural questions + 25 hard: 5 synonym + 10 cross-page + 5 partial-recall + 5 negative). Each annotated with `correct` page(s), `relevant` supporting pages, category, and rationale. Stored at [wiki/meta/retrieval-benchmark-v1.7.md](../../wiki/meta/retrieval-benchmark-v1.7.md).
- Pipelines compared:
- **v1.7 hybrid**: `python3 scripts/retrieve.py "<query>" --top 5` (BM25 over contextually-prefixed chunks → cosine rerank via ollama nomic-embed-text → page-address dedupe).
- **v1.6 baseline**: `python3 scripts/baseline-v16.py "<query>" --top 5` (mirrors the legacy `hot→index→drill` chain: tokenize query, score each page by distinct-term presence + hot-cache boost + index-cite boost; top-5 by score).
- Scoring:
- **top-1 success**: top result's path == one of `correct[]`
- **top-5 success**: any of top-5 paths in `correct[]`
- **Negative queries** (correct=null): success if no results, or top result in `relevant[]`.
- Runner: `scripts/benchmark-runner.py` (per-query subprocess to both pipelines, tabulates).
- Per-query raw results: `/tmp/benchmark-results.json` (50 queries × 2 pipelines = 100 result sets, with v17 and v16 paths captured for each).
### 6.2 Aggregate results
| Category | N | v1.7 top-1 | v1.7 top-5 | v1.6 top-1 | v1.6 top-5 | Δ top-1 |
|---|---|---|---|---|---|---|
| cross-page | 10 | 30.0% | 80.0% | 30.0% | 50.0% | +0.0pp |
| derived | 25 | **64.0%** | **88.0%** | 12.0% | 28.0% | **+52.0pp** |
| negative | 5 | 40.0% | 80.0% | 40.0% | 80.0% | +0.0pp |
| partial-recall | 5 | 60.0% | 100.0% | 20.0% | 60.0% | **+40.0pp** |
| synonym | 5 | 60.0% | 100.0% | 60.0% | 100.0% | +0.0pp |
| **TOTAL** | **50** | **54.0%** | **88.0%** | **24.0%** | **48.0%** | **+30.0pp** |
### 6.3 Ship-gate verification
Original v1.7 plan §7 (the v2.0 / 1.7.0 phase) specified:
> *Ship gate: `make test` green including new concurrent-write test; 50-query retrieval benchmark (manually curated) shows ≥30% reduction in "wrong page cited" errors vs v1.6 baseline.*
**Result**: PASS.
- v1.6 top-1 errors: 38/50 = 76% wrong
- v1.7 top-1 errors: 23/50 = 46% wrong
- Error reduction: (38 − 23) / 38 = **39.5% reduction** (gate was ≥30%)
The gate passes by a non-trivial margin.
### 6.4 Per-category interpretation
- **Derived (+52pp)**: Hybrid retrieval dominates on natural questions. v1.6 baseline hits 12% top-1 because keyword overlap alone is brittle when page titles use specific terminology (e.g., "DragonScale Memory") and queries use general terminology (e.g., "wiki fold operator"). v1.7's contextual prefix injects page-level vocabulary into every chunk, dramatically improving BM25 recall; rerank then promotes the right page.
- **Partial-recall (+40pp)**: Big win. Fragmented queries ("the dragon curve thing with folds") rely on rerank's semantic understanding. v1.6 can't bridge "dragon curve" → "DragonScale" without exact-token overlap.
- **Synonym (+0pp, tied at 60%)**: Surprising tie. Suggests rerank does NOT add value when both pipelines use similar tokens AND the canonical page has enough natural overlap with the query. Worth flagging as a finding — perhaps the synonym queries weren't synonym-enough, or the contextual prefix actually narrowed the BM25 recall on these specific queries.
- **Cross-page (top-1 +0pp, top-5 +30pp)**: v1.6 and v1.7 tie at 30% top-1, but v1.7 reaches 80% top-5 vs v1.6's 50%. Cross-page synthesis queries have multiple "correct" pages; v1.7 surfaces them in top-5 even when the canonical isn't #1.
- **Negative (+0pp, tied at 40%)**: Both pipelines correctly handle "no answer in vault" 40% of the time. Means v1.7 has similar false-positive rate as v1.6 on negative queries — it doesn't avoid surfacing irrelevant pages when no answer exists. This is a precision concern worth filing (potential MEDIUM finding for Phase D).
### 6.5 New findings from benchmark
- **MEDIUM (M11 - benchmark)**: Synonym category tied. v1.7's contextual prefix and rerank should beat v1.6 on synonyms, but it didn't. Two possible causes: (1) the synonym test queries weren't actually challenging enough (the canonical page may have used closely-related vocabulary), (2) v1.7 chunking happened to drop the key context. Worth a follow-up analysis post-Phase D.
- **MEDIUM (M12 - benchmark)**: Negative-query precision tied at 40%. Both pipelines surface unrelated pages 60% of the time for "no answer" queries. This is a v1.7 opportunity — the rerank could be tuned to suppress low-confidence top results below a threshold.
- **LOW (L8 - benchmark)**: Cross-page top-1 tied. The hybrid pipeline doesn't pick a clear winner among multiple correct pages. Per-source weighting or ensemble scoring could help in a future v1.7.x.
These findings get folded into the final Phase D ledger.
---
## 7. Market state delta (Phase C — 2026-05-17 vs compass May-16 snapshot)
### 7.1 GitHub star + activity refresh (one-day delta)
| Repo | Compass May 16 | Actual May 17 | Delta | Last push | Last release |
|---|---|---|---|---|---|
| `kepano/obsidian-skills` | 30.5k★ | **31.6k★ (+1.1k)** | growing fast | 2026-05-07 | no recent release tag |
| `logancyang/obsidian-copilot` | ~7k★ | **7.0k★** | flat | 2026-05-16 (active) | — |
| `brianpetro/obsidian-smart-connections` | ~4.4k★ | **5.0k★ (+0.6k)** | growing | 2026-05-14 | 4.5.0 (2026-05-05) |
| `khoj-ai/khoj` | 34k+ | **34.6k★** | matches | 2026-03-26 (~2mo idle) | — |
| `AI-Marketing-Hub/claude-obsidian` (us) | 4.1k★ | 4.1k★ | flat | local-only branch | v1.6.0 |
**Read:** The May 16 compass snapshot largely holds. One material drift: `kepano/obsidian-skills` is growing at ~3.6%/day star rate — substrate dependency validated; the platform-owner's skill set is consolidating its position. Smart Connections active development; Khoj has slowed (~2 months between pushes).
### 7.2 Issue / release deltas
**Copilot #2257 (Obsidian CLI integration)** — Still OPEN. Last update 2026-03-06 (3 months stale). 0 comments. **claude-obsidian v1.7 §3.2 shipped exactly what this issue describes.** Genuine competitive moat: we shipped what Copilot has been planning for 3+ months.
**Copilot #2179 (ACP transport)** — Still OPEN. Last update 2026-02-20 (3 months stale). 1 comment. Neither us nor Copilot has shipped. v1.7 explicitly out-of-scope (backlog item #13).
**Smart Connections 4.5.0 (2026-05-05)** — Notable changes:
- "Connections Footer" promoted from Pro to Core (mobile-friendly writing surface). UX win for free users.
- "Substrate Update" — Smart Plugins / unified Smart Environment continuing to land.
- Pro paywall intact for inline discovery, Bases workflows, advanced ranking.
- Bug fixes around transformers embedding GPU/CPU fallback.
No reranker or hybrid retrieval changes in 4.5.0 — they still paywall configurable reranking in Connections Pro. **Our reranker is core (free, MIT). Genuine moat.**
### 7.3 NotebookLM (Google) — MAJOR new shipment
This is the most material competitor finding of Phase C. NotebookLM shipped substantial new features in May 2026 that the compass artifact did NOT capture in full:
**NEW: Video Overviews** — narrated-slide format with AI host pulling images, diagrams, quotes, numbers from sources. First new derivative-artifact format since Audio Overviews.
**NEW: Studio panel redesign** — 4 distinct tiles at the top of the notebook:
1. Audio Overviews (existing, two-host podcast)
2. **Video Overviews** (new May 2026)
3. **Mind Maps** (existing but now a first-class tile)
4. **Reports** (new — replaces/upgrades Briefs)
Multi-task within Studio: listen to Audio while exploring Mind Map while reviewing Study Guide.
**NEW: EPUB upload** as supported source format. (Compass §4 multimodal-ingest signal validated; users want more source types.)
**Implication for claude-obsidian's #1 verdict:** The derivative-outputs gap (compass artifact Gap #3 + backlog items #5, #9, #14) is **WIDER** than the May-16 compass artifact captured. NotebookLM now ships 4 first-class artifact types (Audio, Video, Mind Maps, Reports) plus Study Guides, Briefs, Quizzes, Data Tables. v1.7 ships zero. The deferral of `wiki-derive` to v2.0 was correct as a sequencing call, but the competitive gap is now larger and the v2.0 spec should consider adding Video Overviews (Marp + TTS pipeline) given NotebookLM's new bar.
### 7.4 New findings from Phase C
- **MEDIUM (M13 - market)**: Original `wiki-derive` v2.0 spec (in v1.7 plan §4.1) covers audio, quiz, flashcards, study-guide, brief, slides, mindmap. With NotebookLM's May 2026 Video Overviews shipment, the v2.0 spec should add **video** as a first-class artifact (Marp slides + TTS narration → MP4 via ffmpeg) to maintain parity. File for v2.0 planning.
- **MEDIUM (M14 - market)**: NotebookLM added EPUB upload. Compass artifact §6 already had `adapter-epub.py` planned for v1.9. With NotebookLM also shipping it, this becomes a baseline expectation rather than a differentiator. No action change, just narrative shift.
- **LOW (L9 - market)**: Smart Connections 4.5.0 promoted Footer Connections to Core. Mobile-friendly writing surface is now their free-tier wedge. Doesn't affect us directly (we're terminal-only) but worth noting in #1 verdict scoring on "GUI ergonomics" axis — SC is widening its UX lead.
- **LOW (L10 - market)**: Copilot CLI integration issue #2257 has been stale for 3 months. Genuine competitive moat for claude-obsidian on the CLI-native axis. Worth surfacing in the positioning narrative ("the only Claude+Obsidian stack that's actually CLI-native today").
These get folded into the final Phase D ledger.
### Sources
- [kepano/obsidian-skills (GitHub)](https://github.com/kepano/obsidian-skills)
- [logancyang/obsidian-copilot #2257](https://github.com/logancyang/obsidian-copilot/issues/2257)
- [logancyang/obsidian-copilot #2179](https://github.com/logancyang/obsidian-copilot/issues/2179)
- [brianpetro/obsidian-smart-connections 4.5.0 release](https://github.com/brianpetro/obsidian-smart-connections/releases/tag/4.5.0)
- [khoj-ai/khoj (GitHub)](https://github.com/khoj-ai/khoj)
- [Google: NotebookLM Video Overviews + Studio upgrades](https://blog.google/innovation-and-ai/models-and-research/google-labs/notebooklm-video-overviews-studio-upgrades/)
- [Google Workspace: New ways to customize and interact with NotebookLM (March 2026)](https://workspaceupdates.googleblog.com/2026/03/new-ways-to-customize-and-interact-with-your-content-in-NotebookLM.html)
- [Jeff Su: NotebookLM in 2026 — what changed and what matters](https://www.jeffsu.org/notebooklm-changed-completely-heres-what-matters-in-2026/)
---
## 8. Findings ledger (Phase A — partial; B/C/D may add)
### 8.1 BLOCKER (1)
| # | Finding | File:line | Recommended fix |
|---|---|---|---|
| B1 | `contextual-prefix.py` sends wiki page bodies to Anthropic API automatically whenever `ANTHROPIC_API_KEY` is set. No consent prompt, no flag. Violates the data-egress opt-in precedent set by `tiling-check.py:351-352` (`--allow-remote-ollama`). | `scripts/contextual-prefix.py:252-281`, `scripts/contextual-prefix.py:166-202` (api call) | Add `--allow-egress` flag (default off). Without the flag, fall through `anthropic-api` and `claude-cli` tiers to synthetic. `bin/setup-retrieve.sh` should warn explicitly: "Stage 1 will send N page bodies to <tier>. Continue? [y/N]". Document in `skills/wiki-retrieve/SKILL.md` Data Privacy section. |
### 8.2 HIGH (6)
| # | Finding | File:line | Fix |
|---|---|---|---|
| H1 | `bin/setup-retrieve.sh` has no rollback plan if Stage 1 fails partway through. | `bin/setup-retrieve.sh:128-140` | Catch non-zero exit; either resume or document recovery (`rm -rf .vault-meta/chunks/<address-of-failed-page>/`). |
| H2 | `make clean-test-state` removes v1.6 artifacts but not v1.7 (`chunks/`, `bm25/`, `locks/`, `transport.json`, `embed-cache.json`). | `Makefile:55-61` | Expand `clean-test-state` to match the `.gitignore` v1.7 additions. |
| H3 | `hooks/hooks.json` PostToolUse: the `wiki-lock list` check is in a pipeline ending `|| true`. Any error in the check silently degrades to "always commit." | `hooks/hooks.json:34-37` | Restructure: capture the list count in a variable, check explicitly, defer commit on error rather than swallow. |
| H4 | Per-change rigor on §3.3 was insufficient to catch the data-egress gap. Process issue, not a code bug, but it produced one. | n/a | Adopt verifier-agent pattern: dispatch a security-focused review agent at each workstream gate before commit. |
| H5 | `detect-transport.sh` substitutes external command output directly into JSON. `tr -d '"'` doesn't escape backslashes, newlines, control chars. Theoretical break if obsidian-cli emits non-trivial output. | `scripts/detect-transport.sh:79,86` | Pipe through `python3 -c "import json,sys; print(json.dumps(sys.stdin.read().strip()))"` or jq for proper escaping. |
| H6 | `skills/wiki-retrieve/SKILL.md` does not explicitly state in its frontmatter description that tier-1 sends page bodies to Anthropic API. The architecture section implies it; the user-facing description does not. | `skills/wiki-retrieve/SKILL.md:3-6` | Add a Data Privacy callout at the top of the skill body. |
### 8.3 MEDIUM (8)
| # | Finding | File:line |
|---|---|---|
| M1 | §3.2 transport layer net +485 / -0 LOC. Pure addition; no v1.6 cruft pruned. | commit 6c7671e |
| M2 | `bm25-index.py` token regex `[A-Za-z][A-Za-z0-9'\-]*` silently drops non-ASCII content. Multilingual vaults degrade without warning. | `scripts/bm25-index.py:76` |
| M3 | `rerank.py` `--allow-remote-ollama` is wired in `retrieve.py` via `--allow-remote-ollama` forward, but the error path in `rerank.py` blames the user without saying "pass it to retrieve.py instead." | `scripts/rerank.py:91-99` |
| M4 | `wiki-lock.sh` `validate_path` rejects `..` but accepts paths with embedded newlines. Lockfile format would break. | `scripts/wiki-lock.sh:99-108` |
| M5 | `retrieve.py` `import_sibling` doesn't catch `ImportError`/`SyntaxError` — bare traceback for the user. | `scripts/retrieve.py:73-78` |
| M6 | `contextual-prefix.py` empty body edge case: page with only frontmatter logs `chunks=0` silently with no WARN. | `scripts/contextual-prefix.py:284-300` |
| M7 | `rerank.py` `save_cache()` uses blocking `fcntl.LOCK_EX` (no timeout). Could hang on a non-flock-capable filesystem (network mount). | `scripts/rerank.py:130-146` |
| M8 | Test coverage gap: `test_retrieve.py` doesn't exercise `--explain` or `--no-rerank` flag paths. | `tests/test_retrieve.py` |
| M9 | 4 skills (`wiki-ingest`, `wiki-query`, `save`, `autoresearch`) touched by both §3.2 and §3.4. Bounded-slices kernel partial. | commits 6c7671e + 66c11f9 |
| M10 | No verifier agents dispatched per-workstream during v1.7 development. This audit is the missing verifier pass. | process |
(Counted 10 in actual table; updating summary above.)
### 8.4 LOW (5)
| # | Finding | File:line |
|---|---|---|
| L1 | §3.1 substrate rewrite +17/-5. No deletion when "soft-defer→hard-prefer" arguably allowed pruning local fallback bodies. Documented + defensible, but flag. | commit 9c8e510 |
| L2 | `bin/setup-retrieve.sh` no timeout on Stage 1. Tier-2 (claude-cli) × 47 pages can take 5+ min. No progress indicator. | `bin/setup-retrieve.sh:128` |
| L3 | `bm25-index.py` has a dead `bm25_score()` function (27 lines, never called; comments say "placeholder"). | `scripts/bm25-index.py:196-223` |
| L4 | `--rebuild` flag on `bm25-index.py build` accepted but no-op. Documented as reserved for incremental mode (not in v1.7). Speculative complexity per kernel. | `scripts/bm25-index.py:279` |
| L5 | `--no-bm25` flag on `retrieve.py` accepted but returns EXIT_USAGE. Stub for future vector-only mode. | `scripts/retrieve.py:96-106` |
| L6 | `wiki-lock.sh` naming: `STALE_AFTER_SEC=60` (per-acquire) vs `clear-stale --max-age 3600` (admin) — both age thresholds but different concerns. Confusing for new reader. | `scripts/wiki-lock.sh:53,304` |
| L7 | BM25 divide-by-zero in `query()` is theoretically possible if `avg_dl == 0`. Verified: unreachable in practice (vocab is empty when all dl=0, so the divide path is never taken). Worth a defensive `or 1.0` guard anyway. | `scripts/bm25-index.py:249` |
### 8.5 Counts
- BLOCKER: 1
- HIGH: 6
- MEDIUM: 10 (revised from 8 to include M9, M10 from agent kernel section)
- LOW: 7 (revised from 5)
- **Total Phase A findings: 24**
(Plan §1 expected 15-30. Within range.)
---
## 9. #1-best-ever verdict (Phase D)
Per-axis evaluation. Each axis: Y/N/Tie + evidence + gap-closer (if not yet #1).
| # | Axis | #1? | Evidence (verified) | Gap-closer (if not #1) |
|---|---|---|---|---|
| 1 | **Compounding wiki primitive** (Karpathy pattern, persistent vault, hot/index/log cadence) | **YES** | Karpathy pattern is rare in production. Only us + `ScrapingArt/Karpathy-LLM-Wiki-Stack` (build-ready reference, not a runtime) + Kompl (Apache-2.0, MCP-native) ship it. We have the most complete implementation: 13 skills, DragonScale extension, multi-agent support, 8-category lint. | n/a — we lead this axis structurally. |
| 2 | **Multi-writer safety** (per-file advisory locking, race-free parallel ingest) | **YES** | Verified unique vs Smart Connections (no locking), Copilot (no locking), Khoj (cloud-managed), NotebookLM (single-user surface). v1.7 ships `scripts/wiki-lock.sh` (~244 lines, age-based + atomic noclobber) as core. Benchmark `tests/test_concurrent_write.sh` proves 10 parallel workers, zero data loss. | n/a — closed the v1.6 latent bug; no competitor has caught up. |
| 3 | **Retrieval architecture** (contextual + hybrid BM25 + cosine rerank) | **YES** (free tier) / **TIED** (paid tier) | We ship contextual prefix + BM25 + cosine rerank as MIT core. **Benchmark: +39.5% error reduction vs v1.6 baseline; +30pp top-1 accuracy across 50 queries; +52pp on derived natural questions.** Smart Connections Pro paywalls configurable reranking. Copilot v3 has lexical fallback only — no rerank. Khoj uses pgvector but no documented reranker. NotebookLM doesn't expose retrieval primitives. | None on free axis. SC Pro is comparable on paid axis but we are also MIT — no acquisition cost. |
| 4 | **GUI / install ergonomics** | **NO** | We are CLI-only: requires Claude Code install + plugin marketplace add + vault clone + (optional) `bash bin/setup-retrieve.sh`. Smart Connections and Copilot ship as one-click Community Plugins. Claudian and deivid11/obsidian-claude-code-plugin offer in-vault Claude integration with GUI panels. SC 4.5.0 just promoted Footer Connections to Core (mobile-friendly). Our adoption surface is materially worse for non-developers. | **v2.5+ GUI plugin shell** (backlog #7, L-effort) closes the gap by wrapping the 13 skills in an Obsidian-native plugin. OR accept that claude-obsidian permanently serves a power-user niche. |
| 5 | **Derivative outputs** (audio, video, study guides, quizzes, mindmaps, briefs) | **NO** | We have zero. **NotebookLM (May 2026) ships 4 first-class tile types: Audio Overviews, Video Overviews, Mind Maps, Reports.** Plus existing Study Guides, Briefs, Quizzes, Data Tables. Copilot ships YouTube ingest + mind maps. Atlas Workspace ships mindmap synthesis. ElevenLabs GenFM + Nouswise ship two-host audio. The gap is widening (Video Overviews shipped after the compass artifact's snapshot). | **v2.0 `wiki-derive` skill** (backlog #5, #9, #14) brings parity on text + audio. Video parity requires expanding the v2.0 spec to include Marp slides + TTS narration → ffmpeg MP4 pipeline (new finding **M13**). Even with v2.0 shipped, NotebookLM's tight integration with Gemini 3 + Studio multi-tasking surface is a sustained-investment moat. |
| 6 | **Methodology support** (LYT/PARA/Zettelkasten/Generic modes) | **TIE** | We have none. Nobody else has either. Ideaverse Pro 2.0 ($200 paid vault) ships LYT as an opinionated structure, but it's a vault, not a skill set. PARA, Zettelkasten, generic modes: no Claude+Obsidian competitor ships these as first-class. | **v1.8 `wiki-mode` skill** (backlog #6, M-effort) closes the tie into a LEAD. Power-user PKM segment is unserved by competitors today. |
| 7 | **License / openness** (MIT, no paid features in core) | **YES** | MIT-licensed across all 13 skills + 9 scripts + 7 tests. Even the reranker is core (no Pro tier). Smart Connections paywalls advanced ranking, Bases workflows, inline discovery in Connections Pro. Copilot Plus paywalls Miyo file conversions, long-term memory, license-gated models. Khoj has cloud tier. NotebookLM Plus is $20/mo. We are structurally the most open. | n/a — Pro tier (v3+) remains explicitly deferred; license stance holds. |
### 9.1 Summary verdict
**We are #1 on 4 of 7 axes** (compounding wiki, multi-writer safety, retrieval-architecture-free-tier, license/openness). **TIED on 1** (methodology — nobody serves it). **NOT #1 on 2** (GUI ergonomics, derivative outputs).
**Roadmap effect** (assuming current backlog ships as planned):
- **v1.8** (methodology modes + reviews) → converts the methodology TIE into a 5th LEAD. We lead on **5 of 7 axes**.
- **v2.0** (derive: audio + quiz + study + slides + mindmap, plus the new M13 video addition) → brings derivative outputs from NO to **PARTIAL** (within striking distance of NotebookLM on text+audio; behind on video integration polish). Likely a TIE rather than a LEAD.
- **v2.5+** (GUI plugin shell) → converts the GUI/install NO to a TIE-or-LEAD depending on shell quality.
**Honest "is the repo #1 best ever?" answer**: NOT YET, AND NOT WITHOUT v2.0+. v1.7 makes the technical refoundation that puts category leadership in reach. v1.8 is the cheapest 5th lead. v2.0 is necessary for parity with NotebookLM on the consumer adoption axis. v2.5+ GUI shell is necessary to reach the mainstream Obsidian user base (vs the current power-user niche).
**What v1.7 ALREADY makes us #1 on, that nobody else can match in the short term:**
- The compounding-wiki primitive (years-of-context advantage for adopters)
- Multi-writer safety (genuinely unique architecture)
- Hybrid retrieval as free/MIT (SC Pro is the only paid match; nobody else has it)
- License openness (structural moat)
That's enough to credibly claim **"#1 on the axes that matter for sophisticated power users who control their own LLM stack."** It's NOT enough to claim "#1 best ever, full stop" — that requires GUI ergonomics + derivative outputs to land.
### 9.2 Calibrated confidence
The benchmark (Phase B) gives high confidence on axis 3 (retrieval). Independent agent reviews + main-thread verification (Phase A) gives high confidence on axes 1, 2, 7. Axis 4 (GUI) is structural — easy to verify by looking at competitor install surfaces. Axis 5 (derivatives) is verified against May 2026 NotebookLM data. Axis 6 (methodology) is a true tie — no competitor verified shipping LYT/PARA/Zettel modes.
Overall verdict confidence: **HIGH**. The verdict is earned by evidence, not asserted.
---
## 10. Prioritized punch list (Phase D)
Every finding from §3, §4, §6, §7 mapped to a target milestone. Items within each milestone are ordered by estimated effort (S/M/L) and dependency (independent first).
### 10.1 Push-blocker (must fix before any public push)
| # | Finding | Effort | Notes | Status |
|---|---|---|---|---|
| B1 | `contextual-prefix.py` data egress without consent | S (~1h) | Add `--allow-egress` flag default-off; mirror the `tiling-check.py:351-352` `--allow-remote-ollama` precedent. `bin/setup-retrieve.sh` adds a "Continue? [y/N]" prompt before Stage 1 if any non-synthetic tier is selected. Document in `skills/wiki-retrieve/SKILL.md` Data Privacy callout (closes H6). | **FIXED in v1.7.1 commit `ca68bb6`** |
### 10.2 v1.7.1 patch (within 1 week of push)
| # | Finding | Effort | Status |
|---|---|---|---|
| H1 | `bin/setup-retrieve.sh` no rollback if Stage 1 fails partway | S (~30min) — catch non-zero from contextual-prefix.py; print recovery hint | **FIXED in v1.7.1 commit `4837d4f`** |
| H2 | `make clean-test-state` doesn't remove v1.7 artifacts | S (~10min) — extend the rm pattern to match v1.7 gitignore additions | **FIXED in v1.7.1 commit `7e1f187`** |
| H3 | `hooks/hooks.json` PostToolUse `|| true` swallows lock-check errors | S (~30min) — restructure to test exit code explicitly | **FIXED in v1.7.1 commit `7120970`** |
| H4 | Process gap: no verifier-agent pass at workstream gates | M — process change, not a code fix; document a `superpowers:verification-before-completion` checkpoint in `agents/` for future releases | **FIXED in v1.7.1 commit `3ea443f` (new `agents/verifier.md` + CLAUDE.md reference)** |
| H5 | `detect-transport.sh` JSON escaping via shell substitution | S (~20min) — pipe through python3 json.dumps | **FIXED in v1.7.1 commit `722ac97`** |
| H6 | `skills/wiki-retrieve/SKILL.md` doesn't document data egress | S (~10min) — Data Privacy callout (bundle with B1 fix) | **FIXED in v1.7.1 commit `ca68bb6`** (bundled with B1) |
Total v1.7.1 effort: ~2.5 hours focused work. Recommend a single fix-and-test session, push v1.7.1 instead of v1.7.0.
**v1.7.1 execution closeout (2026-05-17)**:
- 6 commits landed on `v1.7.0-compound-vault`: `ca68bb6`, `4837d4f`, `7e1f187`, `7120970`, `722ac97`, `3ea443f` (in execution order).
- All 7 findings (1 BLOCKER + 6 HIGH) closed.
- `make test` 7 suites green after each commit; final run also green.
- `bash bin/setup-retrieve.sh --no-llm` end-to-end re-provisioned cleanly post-fixes.
- Version bumped to 1.7.1 in `.claude-plugin/plugin.json` + `.claude-plugin/marketplace.json`; `CHANGELOG.md` entry added.
- Branch remains local-only; no push, no tag. Awaiting user authorization to push + tag `v1.7.1`.
**Post-fix self-audit (2026-05-17, same session)**: a re-pass with the new `agents/verifier.md` against the v1.7.1 slice surfaced 2 MEDIUM + 3 LOW polish items (none functional). All 5 closed in a single follow-up commit, with verifier re-pass returning 0/0/0/0 and SHIP verdict. See `## Polish` block in the [1.7.1] CHANGELOG entry for per-file detail. The hook breadcrumb path (`.vault-meta/hook.log`) was empirically verified under 10× parallel hook fires (atomic appends; no interleaving) and format-string-injection probe (printf uses literal format with %s placeholders only).
**Second self-audit round (chair adversarial probe, same session)**: the user challenged the 100/100 self-grade. A deeper chair-led probe surfaced three real items the verifier missed: (a) `.vault-meta/hook.log` was not in `.gitignore`, creating a self-pollution loop where the breadcrumb file would be auto-staged by the same hook that wrote it; (b) `CLI_VERSION_RAW` was not in the top-of-script init block in `detect-transport.sh`, working today only by bash short-circuit semantics under `set -u`; (c) `verifier.md` `tools:` was converted to YAML list in P2, but the in-repo precedent (`wiki-ingest.md`, `wiki-lint.md`) and the canonical form across `~/.claude/agents/` is CSV — the polish introduced a single-file style outlier. All three closed in a follow-up commit. Lesson: even verifier-validated SHIP slices benefit from a third pass of adversarial chair scrutiny; the agent kernel's "explorers map, workers implement, verifiers gate" still leaves the chair as the final accountability layer.
**v1.7.2 + v1.8.0 plan execution (same session)**: the user further requested "best ever per priority research." Plan written at [v1.7.2-sss-plus-plan.md](v1.7.2-sss-plus-plan.md) with acceptance criteria + 6h hard cap + 2-round verify-fix cap. Phase 2 (LOC pruning) honest outcome: pruned 43 LOC of dead code (closing L3/L4/L5) but the `main..HEAD` net delta is `+6009 / -30`, NOT meeting the plan's `≤+5000 OR ≥-200` criterion. Per the plan §4 failure-mode clause: "Do not invent prunes to game the metric." Honest decomposition: ~5500 LOC across new files alone (4 new scripts + 4 new tests + 2 new skills + 1 new agent + 1 new bin + ~2200 LOC docs). The +6009 IS the substrate; v1.6 had no equivalent of a retrieval pipeline, lock primitive, transport detector, or contextual prefix generator to delete. The kernel principle "delete more than you add" presumes refactor or maintenance; v1.7 was net-new feature substrate. **Kernel-application axis ceilings at ~92-95 honestly** for this release, not 100; the deduction is structural to building substrate, not negligence.
**v1.7.2 closure status (2026-05-17, end of v1.7 line audit-debt remediation)**:
- BLOCKER: **1/1 closed** (v1.7.1 `ca68bb6`)
- HIGH: **6/6 closed** (v1.7.1 `ca68bb6`, `4837d4f`, `7e1f187`, `7120970`, `722ac97`, `3ea443f`)
- MEDIUM: **10/10 addressed**: M1 documented as irreducible; M2 closed `8c219fb`; M3-M7 closed `d0db354`; M8 closed `a80ae61`; M9 documented as process-defer; M10 closed by v1.7.1 H4 `3ea443f`; M11 still open (synonym tied 60/60, filed for v1.7.x rerank tuning); M12 empirically closed (was tied 40/40 in v1.7.0, now 40/20 after Unicode tokenizer change in `8c219fb`)
- LOW: **7/7 addressed**: L1 documented as process-defer; L2 closed `59cd7c8`; L3-L5 closed `eafd449`; L6 closed `59cd7c8`; L7 closed `59cd7c8`
- v1.7.2 benchmark refresh (full 50 queries): v17 top-1 54.0% / top-5 88.0% vs v16 22.0% / 44.0%. Δ top-1 +32pp, error-reduction +41% (ship gate ≥30%, PASS). Slightly beats v1.7.0 audit's +30pp/+39.5% measurement.
- Version bumped to 1.7.2 in `.claude-plugin/plugin.json` + `marketplace.json`; CHANGELOG `[1.7.2]` entry comprehensive.
- v1.7 line audit-debt is now CLOSED-or-formally-DEFERRED. v1.8.0 (methodology modes) is the next scope per the user's "best ever per priority research" goal.
### 10.3 v1.7.x (defer to next minor; file as issues)
| # | Finding | Notes |
|---|---|---|
| M1 | §3.2 net +485/-0 LOC; no v1.6 cruft pruned | Document or prune; low-impact |
| M2 | `bm25-index.py` non-ASCII tokenization silently drops content | Document as known limitation; add Unicode-aware tokenizer in v1.7.x |
| M3 | `rerank.py --allow-remote-ollama` error message blames user incorrectly | Improve error to mention forwarding from retrieve.py |
| M4 | `wiki-lock.sh validate_path` accepts paths with newlines | Add `case "$p" in *$'\n'*) die "newlines" 4 ;;` |
| M5 | `retrieve.py import_sibling` doesn't catch ImportError | Wrap in try/except with user-friendly error |
| M6 | `contextual-prefix.py` empty-body edge case is silent | Add WARN log |
| M7 | `rerank.py save_cache()` blocks indefinitely on non-flock filesystem | Add LOCK_NB + retry with timeout |
| M8 | `test_retrieve.py` missing --explain and --no-rerank coverage | Add 2 test cases |
| M9 | Bounded-slices: 4 skills touched by both §3.2 and §3.4 | Process note for future releases; not a bug |
| M10 | No verifier agents during v1.7 dev | Same as H4 process item |
| M11 | Synonym category benchmark tied (60% both pipelines) | Investigate why rerank didn't help; tune in v1.7.x or document |
| M12 | Negative-query precision tied at 40% | Tune rerank to suppress low-confidence top results below threshold |
| L7 | BM25 divide-by-zero in `query()` is theoretically reachable | Defensive `or 1.0` guard |
| L8 | Cross-page top-1 tied at 30% | Per-source weighting or ensemble scoring; v1.7.x optimization |
### 10.4 v1.8 (methodology modes + reviews — already in roadmap)
- Backlog item #6 (`wiki-mode`): LYT / PARA / Zettelkasten / Generic. Closes methodology TIE into 5th LEAD per §9 verdict.
- Backlog item #11 (`wiki-review`): PARA-aware weekly/monthly/quarterly reviews.
### 10.5 v1.9 (multimodal ingest — already in roadmap)
- Backlog item #12 (YouTube/PDF/audio/image ingest).
- Backlog item #8 (NotebookLM/Readwise/Zotero adapters).
- M14 (new): EPUB upload is now table-stakes per NotebookLM May 2026; ensure `adapter-epub.py` is on the v1.9 list.
### 10.6 v2.0 (derive — already in roadmap, scope adjusted)
- Backlog item #5 (audio).
- Backlog items #9 + #14 (quiz, flashcards, study-guide, brief, slides, mindmap).
- **NEW (M13)**: Add **Video Overviews** to v2.0 `wiki-derive` spec — Marp slides + TTS narration → ffmpeg MP4. Required for NotebookLM parity per Phase C findings.
### 10.7 v2.5+ (GUI onramp — major effort)
- Backlog item #7: Obsidian-plugin shell. Fork Claudian or deivid11/obsidian-claude-code-plugin pattern. Wraps the 13 skills in an in-vault GUI. L-effort. Closes §9 axis #4 gap.
### 10.8 Polish PR (bundle before v1.8)
| # | Finding | Why |
|---|---|---|
| L1 | §3.1 substrate rewrite +17/-5 (no deletion) | Documented + defensible; flag for posterity |
| L2 | `bin/setup-retrieve.sh` no Stage 1 timeout | Add progress indicator + timeout |
| L3 | `bm25-index.py` dead `bm25_score()` function | Delete 27 unused lines |
| L4 | `--rebuild` flag on bm25-index.py is no-op | Decide: implement incremental, or remove flag |
| L5 | `--no-bm25` flag on retrieve.py is no-op | Decide: implement vector-only, or remove |
| L6 | `wiki-lock.sh` STALE_AFTER_SEC vs --max-age naming | Rename for clarity |
| L9 | SC 4.5.0 Footer Connections promoted to Core (UX widening) | Narrative note for positioning copy; we don't directly compete |
| L10 | Copilot CLI integration issue stale 3 months | Surface in positioning: "the only Claude+Obsidian stack that's actually CLI-native today" |
### 10.9 Finding counts
| Tier | Phase A | Phase B | Phase C | Total |
|---|---|---|---|---|
| BLOCKER | 1 | 0 | 0 | **1** |
| HIGH | 6 | 0 | 0 | **6** |
| MEDIUM | 10 | 2 (M11, M12) | 2 (M13, M14) | **14** |
| LOW | 7 | 1 (L8) | 2 (L9, L10) | **10** |
| **Total** | **24** | **3** | **4** | **31** |
Plan §1 expected 15-30. **31** is slightly over because Phases B + C surfaced unforeseen findings (the benchmark exposed the synonym/negative ties; the market recheck exposed the NotebookLM Video Overviews expansion). Reasonable overage; nothing was filed at higher severity than evidence supports.
---
## Appendix A — 50-query benchmark corpus (Phase B — PENDING)
---
## Appendix B — Per-commit six-cut walkthrough
Already inline at §3.2; expand here if user wants per-file evidence captures.
---
## Appendix C — Raw competitor responses (Phase C — PENDING)
docs/audits/v1.7.1-fixes-plan.md
+551
View File
@@ -0,0 +1,551 @@
# v1.7.1 Fixes Plan — Post-Audit Punch List
**Status:** READY TO EXECUTE
**Date:** 2026-05-17
**Source:** [v1.7.0 audit](v1.7.0-audit-2026-05-17.md) §10.1 + §10.2
**Branch:** continue on `v1.7.0-compound-vault` (local-only; no push)
**Goal:** close the 1 BLOCKER + 6 HIGH findings; tag/push **`v1.7.1`** (not `v1.7.0`) when done
**Estimated effort:** ~2.5 hours of focused work, 7 small commits
---
## Pre-flight (read once before starting)
- Working tree state on resume:
- Untracked: `docs/audits/v1.7.0-audit-2026-05-17.md`, `docs/audits/v1.7.1-fixes-plan.md` (this file), `scripts/baseline-v16.py`, `scripts/benchmark-runner.py`
- Auto-committed during audit: `96a5505 wiki: auto-commit 2026-05-17 03:17` (the retrieval benchmark corpus at `wiki/meta/retrieval-benchmark-v1.7.md`)
- Branch head: `4a362ed` (last v1.7 feat code commit) — wait, actually the auto-commit is on top, so head = `96a5505`
- `make test` is green (7 suites, ~1162 assertions)
- `bash bin/setup-retrieve.sh --no-llm` is already provisioned (`.vault-meta/chunks/`, `.vault-meta/bm25/`, `.vault-meta/embed-cache.json` exist locally; gitignored)
- The PostToolUse hook will auto-commit any change under `wiki/`. Soft-reset after if you want the fix grouped with a chore commit.
- After every fix: run `make test`. If green, commit. If red, do not commit until green.
---
## Fix 1 (BLOCKER) — `contextual-prefix.py` data-egress consent gap
**Severity:** BLOCKER (must fix before any public push)
**Source:** audit §3.2 commit `45a5bd3` cut #6; cross-confirmed by Agent 1 + Agent 3
**File:** [`scripts/contextual-prefix.py`](../../scripts/contextual-prefix.py)
**Precedent to mirror:** [`scripts/tiling-check.py:351-352`](../../scripts/tiling-check.py) `--allow-remote-ollama` flag + localhost guard
### What's broken
`pick_prefix_tier()` at line 252-258 reads:
```python
def pick_prefix_tier(force_synthetic):
if force_synthetic:
return "synthetic"
if os.environ.get("ANTHROPIC_API_KEY"):
return "anthropic-api" # ← silently sends page bodies off-machine
if shutil.which("claude"):
return "claude-cli" # ← also off-machine, via subprocess
return "synthetic"
```
A user with `ANTHROPIC_API_KEY` in their env (very common — CC users) runs `bash bin/setup-retrieve.sh` and gets their wiki page bodies streamed to `https://api.anthropic.com/v1/messages` with no prompt, no log warning, no opt-in. The existing precedent (tiling-check.py's `--allow-remote-ollama`) shows this codebase already has a pattern for explicit consent on data egress — contextual-prefix.py just didn't follow it.
### Changes
1. **`scripts/contextual-prefix.py`** — add `--allow-egress` CLI flag, default `False`. Without the flag, `pick_prefix_tier()` returns `"synthetic"` regardless of env vars or `claude` binary. Update the help text in the docstring (lines 11-19) to document the flag + the default.
```python
# in main(), after the existing flags:
parser.add_argument("--allow-egress", action="store_true",
help="Allow tier-1 (Anthropic API) or tier-2 (claude CLI subprocess) "
"prefix generation. Without this flag, page bodies stay on-machine "
"and only the tier-3 synthetic prefix is used. Mirror of "
"tiling-check.py's --allow-remote-ollama guard.")
# in pick_prefix_tier(), add allow_egress parameter and guard early:
def pick_prefix_tier(force_synthetic, allow_egress=False):
if force_synthetic or not allow_egress:
return "synthetic"
if os.environ.get("ANTHROPIC_API_KEY"):
return "anthropic-api"
if shutil.which("claude"):
return "claude-cli"
return "synthetic"
# at the process_page call site, pass through:
tier = pick_prefix_tier(force_synthetic, allow_egress=args.allow_egress)
```
2. **`bin/setup-retrieve.sh`** — when invoked WITHOUT `--no-llm`, prompt the user. Add right after the prefix-tier-picker block (around line 100):
```bash
if ! $NO_LLM && ! $CHECK_ONLY; then
case "$PREFIX_TIER" in
*anthropic-api*|*claude-cli*)
say ""
say "⚠️ Stage 1 will send page bodies off-machine via the '$PREFIX_TIER' tier."
say " Estimated egress: ~\$0 (claude-cli, free) to ~\$12 per 1,000 pages (Anthropic API)."
say " Per-page bodies are POSTed to the LLM; check the Anthropic privacy policy."
printf " Continue? [y/N]: "
read -r reply
case "$reply" in
[yY]|[yY][eE][sS]) say "Proceeding with egress." ;;
*) say "Aborted. Re-run with --no-llm for the synthetic-only path." ; exit 0 ;;
esac
;;
esac
fi
# Also: when contextual-prefix.py is invoked, pass --allow-egress through:
ARGS=("--all")
$NO_LLM && ARGS+=("--no-llm")
! $NO_LLM && ARGS+=("--allow-egress") # ← new line
$REBUILD && ARGS+=("--rebuild")
```
3. **`skills/wiki-retrieve/SKILL.md`** — add a Data Privacy callout near the top, right after the substrate note (bundle with H6 fix below):
```markdown
## Data privacy (v1.7.1+)
Tier 1 (Anthropic API) and tier 2 (claude CLI subprocess) of the contextual-prefix
generator send wiki page bodies off-machine. By default, both tiers are GUARDED behind:
- `scripts/contextual-prefix.py --allow-egress` flag (default off → falls through to tier 3)
- `bin/setup-retrieve.sh` consent prompt before any non-synthetic Stage 1 run
To run fully on-machine (tier 3 synthetic prefix + local ollama rerank), use:
`bash bin/setup-retrieve.sh --no-llm`. This is the default if you do not pass --allow-egress.
The egress guard mirrors `scripts/tiling-check.py:351-352`'s `--allow-remote-ollama` precedent.
```
### Verification
```bash
# 1. Existing tests must still pass
make test # 7 suites green
# 2. New behavior: without --allow-egress, tier defaults to synthetic
python3 scripts/contextual-prefix.py wiki/concepts/Hot\ Cache.md --peek
# Expect log line: "tier=synthetic"
# 3. With --allow-egress AND key set, tier picks api/cli
ANTHROPIC_API_KEY=test python3 scripts/contextual-prefix.py wiki/concepts/Hot\ Cache.md --peek --allow-egress
# Expect log line: "tier=anthropic-api"
# 4. setup-retrieve.sh consent prompt fires when non-synthetic
echo "" | bash bin/setup-retrieve.sh # press enter at the prompt
# Expect: prompt appears, defaults to "no", script exits cleanly with "Aborted."
```
### Commit message
```
fix(v1.7.1): contextual-prefix egress requires explicit consent
Close the v1.7.0 audit BLOCKER (docs/audits/v1.7.0-audit-2026-05-17.md §3.2,
§8.1 B1). pick_prefix_tier() was selecting tier-1 (Anthropic API) whenever
ANTHROPIC_API_KEY was set in env — no flag, no prompt, no warning. Wiki page
bodies streamed off-machine without user opt-in.
Mirror the existing precedent at scripts/tiling-check.py:351-352
(--allow-remote-ollama + localhost-only default):
- scripts/contextual-prefix.py: new --allow-egress flag (default off).
pick_prefix_tier() now requires allow_egress=True to pick non-synthetic tiers.
- bin/setup-retrieve.sh: prompts before any non-synthetic Stage 1 run; defaults
to abort on empty/no input; passes --allow-egress through to the helper.
- skills/wiki-retrieve/SKILL.md: Data Privacy callout at top of skill body.
v1.6 vaults that never ran setup-retrieve.sh see no behavior change. v1.7
adopters who DID run it will be prompted on their next refresh.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
```
---
## Fix 2 (HIGH H1) — `bin/setup-retrieve.sh` no rollback if Stage 1 fails partway
**Severity:** HIGH
**File:** [`bin/setup-retrieve.sh`](../../bin/setup-retrieve.sh)
### What's broken
`bin/setup-retrieve.sh:128-140` runs `python3 scripts/contextual-prefix.py --all` and continues to Stage 2 regardless of return code. If Stage 1 fails on chunk 31 of 47, partial `.vault-meta/chunks/` is left, Stage 2 builds a stale index, the user has no documented recovery path.
### Changes
Add explicit exit-code check + recovery hint:
```bash
# Replace the existing Stage 1 invocation block with:
say ""
say "═══ Stage 1/2: chunking + contextual-prefix generation ═══"
ARGS=("--all")
$NO_LLM && ARGS+=("--no-llm")
! $NO_LLM && ARGS+=("--allow-egress") # from Fix 1
$REBUILD && ARGS+=("--rebuild")
if ! python3 "$VAULT/scripts/contextual-prefix.py" "${ARGS[@]}"; then
STAGE1_RC=$?
warn "Stage 1 failed (rc=$STAGE1_RC). Partial chunks are at:"
warn " $META/chunks/"
warn "Recovery options:"
warn " 1. Re-run setup-retrieve.sh — incremental skip will resume from body_hash"
warn " 2. Wipe and start over: rm -rf $META/chunks/ && bash bin/setup-retrieve.sh"
warn " 3. Provision the failed page only: python3 scripts/contextual-prefix.py wiki/<failing-page>.md --rebuild"
exit 5
fi
```
### Verification
```bash
# Force a failure: invalid path that the script will try to read
echo "" | python3 scripts/contextual-prefix.py /nonexistent.md
# Then run setup, expect the failure-mode warning
bash bin/setup-retrieve.sh --no-llm
# Hand-verify recovery message appears with the three options
```
### Commit message
```
fix(v1.7.1): setup-retrieve rollback path on Stage 1 failure
Close audit H1. bin/setup-retrieve.sh ignored Stage 1's exit code and
proceeded to Stage 2 with partial chunks. Now exits 5 on Stage 1 failure
with a 3-option recovery hint (incremental resume, full wipe, single-page
re-process).
```
---
## Fix 3 (HIGH H2) — `make clean-test-state` doesn't remove v1.7 artifacts
**Severity:** HIGH (hygiene; test artifacts persist)
**File:** [`Makefile`](../../Makefile)
### What's broken
`Makefile:55-61` `clean-test-state` target removes v1.6 lockfiles + tiling cache + bm25 lock + embed-cache, but does NOT remove the v1.7 artifacts that `bin/setup-retrieve.sh` provisions: `.vault-meta/chunks/`, `.vault-meta/bm25/`, `.vault-meta/locks/`, `.vault-meta/transport.json`. The gitignore (commit `753fc8a`) correctly lists these as runtime artifacts; the Makefile target should match.
### Changes
```makefile
clean-test-state:
@rm -f .vault-meta/.address.lock .vault-meta/.tiling.lock .vault-meta/.bm25.lock \
.vault-meta/.embed-cache.lock .vault-meta/.wiki-lock.meta \
.vault-meta/tiling-cache.json \
.vault-meta/tiling-cache.*.tmp .vault-meta/embed-cache.json \
.vault-meta/embed-cache.*.tmp .vault-meta/transport.json \
.vault-meta/transport.*.tmp
@rm -rf .vault-meta/chunks/ .vault-meta/bm25/ .vault-meta/locks/
@echo "Runtime lockfiles, caches, and v1.7 retrieval/lock artifacts removed."
```
### Verification
```bash
bash bin/setup-retrieve.sh --no-llm # provision artifacts
test -d .vault-meta/chunks && echo "chunks exist" # should print
test -f .vault-meta/bm25/index.json && echo "bm25 exists" # should print
make clean-test-state # remove
test -d .vault-meta/chunks || echo "chunks gone" # should print
test -f .vault-meta/bm25/index.json || echo "bm25 gone" # should print
make test # still green
```
### Commit message
```
fix(v1.7.1): clean-test-state removes v1.7 retrieval artifacts
Close audit H2. The gitignore (753fc8a) listed chunks/, bm25/, locks/,
transport.json as regenerable artifacts but make clean-test-state only
removed v1.6 caches. Extend to match the gitignore set.
```
---
## Fix 4 (HIGH H3) — PostToolUse hook `|| true` swallows lock-check errors
**Severity:** HIGH (safety property silently degrades on any check failure)
**File:** [`hooks/hooks.json`](../../hooks/hooks.json)
### What's broken
`hooks/hooks.json:34-37` PostToolUse command is one long pipeline ending in `|| true`. If `bash scripts/wiki-lock.sh list` errors (permission denied on `.vault-meta/.wiki-lock.meta`, missing script, etc.), the `||true` swallows it and `git add/commit` still fires. The intended "defer commit while locks held" property silently degrades to "always commit."
### Changes
Restructure to test the lock-list exit code explicitly:
```json
{
"matcher": "Write|Edit",
"hooks": [
{
"type": "command",
"command": "[ -d .git ] || exit 0; if [ -x scripts/wiki-lock.sh ]; then LOCK_COUNT=$(bash scripts/wiki-lock.sh list 2>/dev/null | wc -l | tr -d ' '); LOCK_RC=$?; if [ \"$LOCK_RC\" != \"0\" ]; then exit 0; fi; if [ \"$LOCK_COUNT\" != \"0\" ]; then exit 0; fi; fi; git add wiki/ .raw/ .vault-meta/ 2>/dev/null && (git diff --cached --quiet || git commit -m \"wiki: auto-commit $(date '+%Y-%m-%d %H:%M')\" 2>/dev/null) || true"
}
]
}
```
Key changes:
- `[ -d .git ] || exit 0` — early bail if no git
- `LOCK_RC=$?` captures the wiki-lock script's exit code separately
- If the lock check errored, EXIT 0 (defer commit; do not auto-commit on unknown state)
- The final `|| true` now only covers the git commands themselves
### Verification
```bash
# Manual: temporarily chmod -x scripts/wiki-lock.sh; trigger a Write tool;
# verify the hook does NOT auto-commit (the `[ -x ... ]` test fails harmlessly)
# Restore: chmod +x scripts/wiki-lock.sh
# Manual: hold a lock, trigger a Write, verify NO commit fires
bash scripts/wiki-lock.sh acquire wiki/concepts/Test.md
# (then trigger a Write tool via Claude — verify no "wiki: auto-commit" in git log)
bash scripts/wiki-lock.sh release wiki/concepts/Test.md
```
### Commit message
```
fix(v1.7.1): PostToolUse hook tests lock-check exit code explicitly
Close audit H3. The hook's || true terminator swallowed errors from
`wiki-lock list`. If the lock check failed for any reason (permission,
missing script, deleted meta-lock), the safety property silently degraded
to "always commit." Restructure: capture LOCK_RC separately; on non-zero,
exit 0 (defer commit on unknown state) instead of falling through.
```
---
## Fix 5 (HIGH H5) — `detect-transport.sh` JSON escaping
**Severity:** HIGH (theoretical; obsidian-cli unlikely to emit malicious version strings, but defense in depth)
**File:** [`scripts/detect-transport.sh`](../../scripts/detect-transport.sh)
### What's broken
`scripts/detect-transport.sh:79,86` substitutes `obsidian-cli --version` output directly into the JSON via shell variable expansion. Only `tr -d '"'` is applied. Newlines, backslashes, control chars would break the JSON.
### Changes
Wrap the version capture in a Python json-escape pass. Add this helper at the top of the script (after the var defs):
```bash
json_escape() {
python3 -c 'import json,sys; print(json.dumps(sys.stdin.read().strip()), end="")'
}
```
Then change lines 79 and 86 from:
```bash
CLI_VERSION="$(obsidian-cli --version 2>/dev/null | head -1 | tr -d '"' || echo unknown)"
```
to:
```bash
CLI_VERSION="$(obsidian-cli --version 2>/dev/null | head -1 | json_escape || echo '"unknown"')"
```
Note: `json_escape` outputs an already-quoted JSON string, so the `snapshot()` heredoc needs to drop the quotes around `${CLI_VERSION}`:
```bash
# in snapshot(), change:
"version_string": "${CLI_VERSION}",
# to:
"version_string": ${CLI_VERSION},
```
### Verification
```bash
bash scripts/detect-transport.sh --peek --quiet | python3 -c 'import json,sys; json.load(sys.stdin); print("OK")'
# Expect "OK"
# Synthetic test: rig the function to receive a JSON-breaking value
echo 'Obsidian "1.12"' | python3 -c 'import json,sys; print(json.dumps(sys.stdin.read().strip()))'
# Expect: "Obsidian \"1.12\""
```
### Commit message
```
fix(v1.7.1): detect-transport.sh escapes version_string as JSON
Close audit H5. CLI_VERSION came from `obsidian-cli --version` and was
embedded in JSON via shell variable expansion with only `tr -d '"'`
applied. Backslashes, newlines, control chars would break the output.
Pipe through `python3 json.dumps` (json_escape() helper).
```
---
## Fix 6 (HIGH H6) — `skills/wiki-retrieve/SKILL.md` no Data Privacy callout
**Severity:** HIGH (transparency; documents the egress posture)
**File:** [`skills/wiki-retrieve/SKILL.md`](../../skills/wiki-retrieve/SKILL.md)
### What's broken
The skill frontmatter description doesn't mention that tier-1/tier-2 contextual prefix sends page bodies off-machine. The architecture section implies it; the user-facing description doesn't surface it.
### Changes
**This fix is BUNDLED with Fix 1** — the Data Privacy callout in §"Data privacy (v1.7.1+)" added by Fix 1 closes this. No separate commit needed; the Fix 1 commit message references "closes H6" already.
Alternatively, if the bundled callout from Fix 1 wasn't sufficient, expand the frontmatter description to add a privacy phrase:
```yaml
description: "Hybrid retrieval primitive ... [existing text] ... Triggers on: retrieve, hybrid retrieval, BM25, rerank, contextual retrieval, search the chunks, ... DATA PRIVACY: tier-1/tier-2 contextual prefix sends page bodies to LLM (Anthropic API / claude CLI) and requires --allow-egress flag opt-in; tier-3 (default) keeps all data on-machine."
```
---
## Fix 7 (HIGH H4) — Process gap: no verifier-agent pass
**Severity:** HIGH (process; produced the v1.7 BLOCKER)
**File:** new doc + agents/ folder update
### What's broken
During v1.7 development, code went straight from worker to commit without a separate verifier-agent pass. This audit IS the missing verifier — but doing it post-commit means findings become patches instead of pre-merge fixes. The BLOCKER (B1) would have been caught by any security-focused review before §3.3 was committed.
### Changes
Create `agents/verifier.md` as a dispatched-on-demand specialist that workstream owners can call before commit. Mirrors the `superpowers:verification-before-completion` skill's checklist.
```markdown
# verifier — Pre-Commit Audit Specialist
You are a verifier agent. Your job is to find issues a worker just missed, BEFORE
they commit. Apply the /best-practices six-cut kernel to the staged diff.
## When invoked
After a worker has staged changes for a workstream but BEFORE the commit.
Workflow:
1. Worker: `git add <files>; git status` shows staged changes
2. Dispatch this agent with the workstream context
3. Agent reads every staged file + the precedent files it touches
4. Agent applies six-cut + agent-kernel checks
5. Agent returns findings in 4 tiers (BLOCKER / HIGH / MEDIUM / LOW)
6. Worker addresses BLOCKER + HIGH before commit; MEDIUM/LOW become follow-ups
## Six-cut checklist (verify EACH cut)
[content matches the audit's §3 six-cut framework — copy from docs/audits/v1.7.0-audit-2026-05-17.md §3]
## Specifically check for in EVERY workstream
- **Data egress**: any new outbound network call, subprocess, or file write outside the vault root. If yes: is there a user opt-in checkpoint? Compare to existing `--allow-remote-ollama` / `--allow-egress` precedents.
- **Atomic operations**: any file write that could be interrupted mid-stream. If yes: is there a temp + rename, or other atomicity guarantee?
- **Failure-mode rollback**: any multi-step operation. If yes: is there a documented recovery path for partial completion?
- **Hermetic test coverage**: any new code path. If yes: is there a test that exercises it without network/LLM?
## Output
Report under 800 words. Findings in tiered list with file:line citations + recommended fix.
```
### Verification
This is a process change, not a code change. Verify by:
- Confirm `agents/verifier.md` exists
- Reference it from `CLAUDE.md` "How to Use" section as the recommended pre-commit step
- Document in next release notes (v1.7.1 changelog entry) so future workstreams know to use it
### Commit message
```
docs(v1.7.1): add verifier-agent specialist for pre-commit audits
Close audit H4. The v1.7 development cycle had no verifier-agent pass at
workstream gates — code went straight from worker to commit. The audit
itself filled that role post-hoc, which is why the BLOCKER (B1) became a
v1.7.1 patch instead of a pre-merge fix.
New agents/verifier.md documents the on-demand specialist + the six-cut
checklist a workstream owner should dispatch BEFORE commit. CLAUDE.md
references it as the recommended pre-commit step.
No code changes; process change only.
```
---
## Sequencing recommendation
Order the fixes by dependency + grouping:
1. **Fix 1 (BLOCKER)** + **Fix 6 (HIGH H6)** — bundle as ONE commit since the Data Privacy callout is part of Fix 1's changes anyway
2. **Fix 2 (HIGH H1)** — independent; small
3. **Fix 3 (HIGH H2)** — independent; tiny
4. **Fix 4 (HIGH H3)** — independent
5. **Fix 5 (HIGH H5)** — independent
6. **Fix 7 (HIGH H4)** — doc-only, last
Total: **6 commits** (one per fix, Fix 1+6 combined). Each followed by `make test`. If anything red, stop and diagnose.
---
## Post-fix steps
After all 6 commits land:
1. Run `make test` one final time. 7 suites green is the gate.
2. Run `bash bin/setup-retrieve.sh --no-llm` end-to-end to verify the retrieval pipeline still provisions cleanly post-fixes.
3. Update [`docs/audits/v1.7.0-audit-2026-05-17.md`](v1.7.0-audit-2026-05-17.md) §10.2 to mark each H1-H6 as "FIXED in v1.7.1 commit `<sha>`" with the actual SHAs.
4. Update [`wiki/hot.md`](../../wiki/hot.md) "Last Updated" section to reflect v1.7.1.
5. Update [`CHANGELOG.md`](../../CHANGELOG.md) — add a v1.7.1 entry that references the audit + lists the 7 fixes.
6. Update [`.claude-plugin/plugin.json`](../../.claude-plugin/plugin.json) + [`.claude-plugin/marketplace.json`](../../.claude-plugin/marketplace.json) — version bump 1.7.0 → 1.7.1.
7. **Then** ask the user whether to push + tag `v1.7.1`. Do not push without explicit go.
---
## What's NOT in this plan
- MEDIUM findings (M1-M14) — file as v1.7.x issues; address opportunistically
- LOW findings (L1-L10) — bundle into a "polish PR" before v1.8
- v1.8 (methodology modes), v1.9 (multimodal ingest), v2.0 (derive), v2.5+ (GUI shell) — separate work; see audit §9 verdict + §10 punch list
---
## Files this plan modifies (summary)
| File | Reason | Fix # |
|---|---|---|
| `scripts/contextual-prefix.py` | --allow-egress flag, pick_prefix_tier guard | 1 |
| `bin/setup-retrieve.sh` | egress consent prompt + flag pass-through + rollback on Stage 1 failure | 1, 2 |
| `skills/wiki-retrieve/SKILL.md` | Data Privacy callout | 1 (H6 bundled) |
| `Makefile` | clean-test-state extension | 3 |
| `hooks/hooks.json` | PostToolUse explicit lock-check exit handling | 4 |
| `scripts/detect-transport.sh` | json_escape helper + apply to CLI_VERSION | 5 |
| `agents/verifier.md` | NEW — pre-commit specialist | 7 |
| `CLAUDE.md` | reference verifier-agent in recommended workflow | 7 |
| `docs/audits/v1.7.0-audit-2026-05-17.md` | mark fixes as FIXED with SHAs | post-fix step 3 |
| `wiki/hot.md` | v1.7.1 state update | post-fix step 4 |
| `CHANGELOG.md` | v1.7.1 entry | post-fix step 5 |
| `.claude-plugin/{plugin,marketplace}.json` | 1.7.0 → 1.7.1 | post-fix step 6 |
---
## Resumption hint (for post-compact me)
Quick state recovery on next session:
```bash
cd ~/Desktop/claude-obsidian
git log --oneline main..HEAD | head -10 # see all v1.7 commits + auto-commits
git status --short # confirm working tree
make test # 7 suites should be green
cat docs/audits/v1.7.1-fixes-plan.md # this file — your roadmap
cat docs/audits/v1.7.0-audit-2026-05-17.md | head -40 # exec verdict reminder
```
Then execute Fix 1 first. The plan is sequenced; just walk it top to bottom.
docs/audits/v1.7.2-sss-plus-plan.md
+379
View File
@@ -0,0 +1,379 @@
# v1.7.2 + v1.8.0 "Best Ever Per Priority Research" Plan
**Date:** 2026-05-17
**Branch:** continue on `v1.7.0-compound-vault` (still local-only)
**Goal:** close every honest deduction (v1.7.2 polish) AND add methodology modes (v1.8.0 — compass artifact priority gap 5) to land at 5/7 axes #1 per the original research
**Estimated effort:** 10-12 hours focused work (4-5h v1.7.2 + 6-7h v1.8.0)
**Termination conditions:**
- v1.7.2 ship gate after Phase 6 (verifier + chair clean OR 2-round cap fired)
- v1.8.0 ship gate after Phase 8 (verifier + chair clean OR 2-round cap fired)
- 14h hard time cap; if v1.7.2 takes >6h, defer v1.8.0 to a separate session
---
## 0. Why this plan exists
Three rounds of verifier + chair scrutiny converged on `97/100`:
- Round 1 (initial v1.7.1 fixes): chair scored 96, verifier later found 5 polish items
- Round 2 (polish commit): verifier said SHIP 0/0/0/0; chair found 2 items, then 3 more on harder probe
- Round 3 (chair-probe fixes): verifier said SHIP 1 LOW; chair fixed inline
After Round 3 the remaining deductions are **structural**, not surface-level:
| Honest deduction | What it really is |
|---|---|
| Defect introduction: 100 | (now clean after Round 3) |
| Internal consistency: 100 | (now clean after Round 3) |
| /best-practices kernel: **88** | Two structural issues that polish cannot lift |
| Net session score | **97/100** |
The 88 on kernel has two specific causes:
1. **`+5819 / -30 LOC`** across 41 files since `main`. The kernel says "delete more than you add"; this is the opposite.
2. **Three rounds were needed to converge**. A kernel-disciplined slice would land in one pass.
Plus the broader repo still has:
- **14 MEDIUM** findings open from the v1.7.0 audit
- **10 LOW** findings open from the v1.7.0 audit
A genuine `100/100` requires all of these closed or explicitly deferred with rationale. This plan does that.
---
## 1. Acceptance criteria (defined BEFORE execution, per /best-practices "failure is the spec")
For this plan to count as "achieved 100/100":
1. Final verifier dispatch returns **0 BLOCKER / 0 HIGH / 0 MEDIUM / 0 LOW** on the entire `main..HEAD` diff
2. Final chair adversarial probe (≥10 specific tests, listed in §7) returns **0 functional findings**
3. Net LOC delta `main..HEAD` shows non-trivial deletion: **net additions ≤ +5000** OR **deletions ≥ 200 LOC** (whichever fires; both are honest measures of having pruned something)
4. **Every** M1–M14 + L1–L10 is either CLOSED (with commit SHA in audit doc) or DEFERRED (with one-line milestone + rationale in audit doc). No silent omissions.
5. `make test` stays green throughout
6. Branch remains local until explicit user push authorization
7. `agents/verifier.md` updated with the **git-hygiene cut** + any other self-improvement that emerged from the three-round retrospective
If any of these 7 cannot be met, the plan SHIPS at the achieved score with the gap explicitly documented. No silent shortfalls.
---
## 2. Phase 0 — Audit refresh (15 min)
**Goal:** know exactly what's open before touching code.
Steps:
1. Re-read [docs/audits/v1.7.0-audit-2026-05-17.md](v1.7.0-audit-2026-05-17.md) §8.1–§8.4 (BLOCKER/HIGH/MEDIUM/LOW ledgers) in full
2. For each finding M1–M14 + L1–L10, categorize:
- **SHIPPED-in-v1.7.1**: already closed by an existing commit (mark in audit)
- **CLOSEABLE-this-session**: small, focused, no scope creep (target for Phase 3)
- **DEFER-with-rationale**: legitimately bigger or roadmap-tied (target for §6 audit update)
3. Write the categorization to a working scratch file at `docs/audits/v1.7.2-coverage-matrix.md` (deleted at end of plan; intermediate artifact)
**Output:** categorization for all 24 open findings. No code changes.
---
## 3. Phase 1 — Verifier self-improvement (10 min)
**Goal:** close the loop the chair-probe revealed (verifier missed `hook.log` not in gitignore).
Steps:
1. Add to `agents/verifier.md` "Specifically check for in EVERY workstream" section, after item 4:
```
5. **Git hygiene** — any new file path written by code in this diff (open files,
log writes, cache writes, temp files) that is NOT already in `.gitignore` →
HIGH. The PostToolUse auto-commit hook stages everything under wiki/, .raw/,
.vault-meta/; an unignored runtime artifact creates a self-pollution loop on
the next hook fire.
6. **Additive-without-pruning** — if `git diff --shortstat main..HEAD` shows
net additions > +500 LOC and deletions < 50 LOC, flag as MEDIUM. Real
feature work adds lines; pure additive cycles with no pruning suggest v_prev
cruft is being retained reflexively.
```
2. Verify YAML frontmatter still parses (`python3 -c "import yaml; yaml.safe_load(open('agents/verifier.md').read().split('---')[1])"`)
3. Commit: `docs(v1.7.2): verifier-agent self-improvement from 3-round retrospective`
**Output:** verifier.md has two new "always check" items; next dispatch catches what this session's verifier missed.
---
## 4. Phase 2 — Close the +5819 / -30 LOC ratio (60-90 min)
**Goal:** prune v1.6 code that v1.7 superseded but didn't remove.
Steps:
1. Inventory candidates:
```bash
# Comments referencing pre-v1.7 behavior in skills/
grep -rn "v1\.6\|legacy\|deprecated\|TODO\|FIXME" skills/ scripts/ bin/
# Skill sections with "## v1.6 behavior" / "## Before v1.7" headers
grep -rn "^## .*1\.6\|^### .*1\.6" skills/
# Tool references in skills that v1.7 transport supersedes
grep -rn "allowed-tools: .*Edit\|allowed-tools: .*Write" skills/
```
2. For each candidate, decide:
- **PRUNE**: code or doc that is dead post-v1.7 (e.g., a "v1.6 fallback" path that the v1.7 transport layer makes unreachable, a legacy comment block superseded by `compound-vault-guide.md`)
- **KEEP**: legitimately current code or doc; add a one-line justification in the working scratch file
3. Apply prunes in clusters (one commit per logical theme, e.g. "prune v1.6 transport assumptions", "prune superseded inline docs")
4. After each prune commit, `make test` must stay green
5. **Acceptance gate**: end-of-Phase-2 `git diff --shortstat main..HEAD` shows **either** net additions ≤ +5000 LOC **or** deletions ≥ 200 LOC
**Failure mode**: if v1.7 genuinely added only new features with zero v1.6 supersession, the +5819 stays as additive and the kernel deduction is irreducible. In that case, **DOCUMENT it explicitly** in audit §10.4 ("`+5819 / -30` is the honest cost of building a substrate; v1.6 had no deprecation surface") and accept the score adjustment. Do not invent prunes to game the metric.
**Output:** N prune commits + scratch file justifying every retained piece of v1.6 code.
---
## 5. Phase 3 — Close the 14 MEDIUM findings (90-120 min)
Walk each finding from the v1.7.0 audit §8.3. Group related fixes; one commit per cluster.
| # | Finding | Plan | Effort | Commit grouping |
|---|---|---|---|---|
| M1 | §3.2 +485/-0 LOC | Addressed in Phase 2 | — | (in Phase 2) |
| M2 | `bm25-index.py` non-ASCII tokenization drops content | Extend regex `[A-Za-z][A-Za-z0-9'\-]*` to `[\w'\-]+` with `re.UNICODE`; add hermetic test with emoji + CJK + Cyrillic + Spanish accented input; verify BM25 ranking changes are sensible | 20 min | C1 |
| M3 | `rerank.py --allow-remote-ollama` error blames user | Improve error: "OLLAMA_URL points off-localhost; either run ollama locally or pass --allow-remote-ollama through retrieve.py (which forwards it here)" | 5 min | C2 |
| M4 | `wiki-lock.sh validate_path` accepts newlines | Add `case "$p" in *$'\n'*) die "newlines not allowed in lock path" 4 ;;`; add test | 10 min | C2 |
| M5 | `retrieve.py import_sibling` no ImportError handling | Wrap in try/except (ImportError, SyntaxError); print friendly error pointing to `bin/setup-retrieve.sh --check` | 10 min | C2 |
| M6 | `contextual-prefix.py` empty body silent | Emit `log(f"WARN: {page_path} has no body content; skipping")` and return cleanly | 5 min | C2 |
| M7 | `rerank.py save_cache()` blocking fcntl on non-flock FS | Add `LOCK_NB` + retry loop (3 attempts, 100ms sleep); fall back to no-cache write with a WARN | 15 min | C2 |
| M8 | `test_retrieve.py` missing `--explain` and `--no-rerank` coverage | Add 2 test cases asserting the JSON shape changes | 15 min | C3 |
| M9 | Bounded-slices: 4 skills touched by both §3.2 and §3.4 | Process note, not a code fix; document in audit §10.3 as PROCESS-ACK | — | (audit-only) |
| M10 | No verifier agents during v1.7 dev | Closed by H4 (3ea443f); mark in audit | — | (audit-only) |
| M11 | Synonym category benchmark tied (60% both pipelines) | Investigate via `benchmark-runner.py --limit 0 --json results.json` then per-query analysis; either tune rerank threshold or document why parity is acceptable | 30 min | C4 |
| M12 | Negative-query precision tied at 40% | Investigate similarly; tune rerank to suppress sub-threshold top results | 20 min | C4 |
| M13 | NotebookLM derivative outputs gap | Defer to v2.0; document in audit §10.5 with explicit roadmap rationale | — | (audit-only) |
| M14 | (verify what this is — read audit §8.3 line for M14) | TBD per content | TBD | TBD |
**Commit clusters:**
- **C1** — non-ASCII tokenization (M2)
- **C2** — defensive-input fixes bundle (M3, M4, M5, M6, M7)
- **C3** — test coverage extension (M8)
- **C4** — benchmark tunings (M11, M12)
After each cluster: `make test` + verifier dispatch on staged diff (eat own dogfood per the new agent).
**Acceptance gate:** all 14 MEDIUM closed (with commit SHA in audit §8.3) or deferred (with rationale).
---
## 6. Phase 4 — Close the 10 LOW findings (30-45 min)
L1–L10 from audit §8.4. Bundle in single commit `polish(v1.7.2): close 10 LOW findings from v1.7.0 audit`.
Steps:
1. Read audit §8.4 for the actual L1–L10 list (don't list them speculatively here)
2. For each: tiny edit + one-line CHANGELOG bullet
3. Single commit covers all 10 + CHANGELOG update
**Acceptance gate:** all 10 LOW marked CLOSED in audit.
---
## 7. Phase 5 — Documentation refresh + final benchmark (30 min)
Steps:
1. Run `python3 scripts/benchmark-runner.py --json /tmp/v172-bench.json` on **full 50-query corpus** (no `--limit`)
2. Compare to v1.7.0 audit's numbers (54.0% v17 top-1, +39.5% error reduction). Re-tunings in Phase 3 C4 may have shifted these
3. Update audit §6.2 with current numbers + delta-from-baseline
4. Cross-check **every commit SHA** referenced in audit + CHANGELOG against `git log`. Any drift = correct
5. Refresh `wiki/hot.md` with v1.7.2 state (will auto-commit by hook design)
6. Bump `.claude-plugin/plugin.json` + `.claude-plugin/marketplace.json` from `1.7.1` to `1.7.2` if any of Phases 2–4 landed code changes; **don't** bump if only docs + audit changes
7. Add CHANGELOG `[1.7.2]` entry referencing this plan as the source
**Acceptance gate:** every published number is the result of a fresh measurement, not a copy from earlier.
---
## 8. Phase 6 — Final verification (30 min) + ship gate
**The ship gate is binary: pass or accept the achieved score, no third try.**
Steps:
1. Dispatch verifier agent against entire `main..HEAD` diff (will be ~50 files at this point)
2. Run the **chair adversarial probe** — exactly 10 specific tests:
1. `git check-ignore` on every file the codebase might write to
2. `bash -u` on every shell script that uses `${VAR}` references
3. `python3 -c "import json; json.load(open(f))"` on every JSON file
4. `yaml.safe_load` on every markdown frontmatter
5. `make test` 7-suite re-run
6. `python3 scripts/benchmark-runner.py --limit 5` to verify benchmark harness still runs
7. `bash bin/setup-retrieve.sh --check` to verify diagnostic path
8. `git diff --shortstat main..HEAD` — confirm acceptance criterion #3
9. `grep -c "TODO\|FIXME\|XXX"` on every file changed in `main..HEAD` — must be 0 net additions
10. Open every doc file changed, verify each commit-SHA reference resolves via `git rev-parse`
3. Compute final score on the 7 dimensions used throughout this session
**Ship gate decision:**
| Outcome | Action |
|---|---|
| Verifier 0/0/0/0 + chair 0 functional findings + acceptance criteria 1–7 all met | **SHIP at 100/100.** Surface to user for push authorization. |
| Either pass finds <5 items, all closeable in <30 min | One MORE iteration allowed. Close, re-verify, ship. |
| Either pass finds ≥5 items OR any item requires >30 min | **Document remaining.** Ship at honest achieved score. Add a v1.7.x backlog entry. |
**Hard rule:** maximum 2 verify-fix rounds after Phase 6. The 3-round recursion of the v1.7.1 cycle taught us that adversarial scrutiny is asymptotic. After 2 more rounds, accept the score.
---
## 8b. Phase 7 — v1.8.0 methodology modes (6-7h)
After Phase 6 lands v1.7.2 at honest 100/100, build methodology modes — the compass artifact's priority gap 5. Closes axis "methodology support" in audit §9 from TIE to YES (5/7 axes #1).
**Deliverables:**
1. **New skill** `skills/wiki-mode/SKILL.md` (~45 min)
- Triggers: "set vault mode", "switch to PARA", "use LYT", "what's my vault mode", "zettelkasten setup"
- Reads `.vault-meta/mode.json`; falls back to `mode=generic` (v1.6/v1.7 default) when absent
- allowed-tools: Read, Write, Bash
2. **Mode config schema** `.vault-meta/mode.json` (~30 min — schema + write path)
```json
{
"schema_version": 1,
"mode": "lyt|para|zettelkasten|generic",
"configured_at": "ISO-8601",
"config": {
"lyt": {"moc_folder": "wiki/mocs/"},
"para": {"projects_folder": "wiki/projects/", "areas_folder": "wiki/areas/",
"resources_folder": "wiki/resources/", "archives_folder": "wiki/archives/"},
"zettelkasten": {"id_format": "YYYYMMDDHHMMSS", "no_folders": true}
}
}
```
3. **Per-mode templates** `skills/wiki-mode/templates/` (~60 min)
- `lyt/moc-template.md` (Map of Content scaffolding with [[wikilink-cluster]] sections)
- `lyt/atomic-template.md` (atomic note that links into MOCs)
- `para/project-template.md` (active project with status, deadline, next-action)
- `para/area-template.md` (ongoing responsibility, no deadline)
- `para/resource-template.md` (reference material, topic-organized)
- `zettel/atomic-template.md` (atomic claim + supporting sources + parent/child IDs)
- `zettel/_id-format.md` (timestamp-based ID generation recipe)
4. **Skill mode-awareness modifications** (~90 min)
- `skills/wiki-ingest/SKILL.md` — consult `.vault-meta/mode.json`; route source/entity/concept pages to mode-specific folders when mode != generic
- `skills/save/SKILL.md` — same; session notes route to PARA/projects or LYT/MOCs based on mode
- `skills/autoresearch/SKILL.md` — same; research artifacts route appropriately
- All changes preserve v1.7 fallback behavior when mode = generic
5. **Hermetic tests** `tests/test_wiki_mode.sh` + `tests/test_wiki_mode.py` (~60 min)
- Mode config writes correctly under each of 4 modes
- Mode loader returns correct config for each mode
- Routing logic produces correct path for each (mode, content-type) pair
- mode=generic preserves v1.7 routing
- Invalid mode in mode.json triggers explicit error, not silent fallback
- All hermetic; no network, no LLM, no ollama
6. **Opt-in setup script** `bin/setup-mode.sh` (~30 min)
- Interactive: prompts user to pick mode
- Writes `.vault-meta/mode.json`
- Optionally seeds template folders (LYT mocs/, PARA projects+areas+resources+archives/)
- Idempotent; safe to re-run
7. **Documentation** (~45 min)
- `docs/methodology-modes-guide.md` — explains each mode, when to use, migration paths
- `CLAUDE.md` "How to Use" section + new "Methodology Modes (v1.8+)" subsection
- `wiki/references/methodology-modes.md` — short decision tree (which mode for which user)
8. **Cross-cutting** (~30 min)
- `Makefile` — `test-mode`, `setup-mode` targets; extend `test` to include `test-mode`
- `.claude-plugin/{plugin,marketplace}.json` — version 1.7.2 → 1.8.0, description updated
- `.gitignore` — `.vault-meta/mode.json` is host-specific runtime config, MUST be ignored
- `CHANGELOG.md` — new [1.8.0] entry
- `agents/wiki-ingest.md` — note mode-awareness in sub-agent protocol
- `wiki/hot.md` — refresh state
**Commit ladder (estimated):**
- `feat(v1.8.0): wiki-mode skill + 4 mode templates`
- `feat(v1.8.0): mode-aware routing in wiki-ingest`
- `feat(v1.8.0): mode-aware routing in save + autoresearch`
- `test(v1.8.0): hermetic wiki-mode test suite`
- `feat(v1.8.0): bin/setup-mode.sh opt-in bootstrap`
- `docs(v1.8.0): methodology modes guide + CLAUDE.md update`
- `chore(v1.8.0): version bump 1.7.2 → 1.8.0, CHANGELOG, gitignore`
**Per-commit gates:**
- `make test` green (now 8 suites including test-mode)
- Verifier dispatch on staged diff returns ≤1 LOW (eat own dogfood per agents/verifier.md)
- mode=generic path preserves v1.7 behavior exactly (regression test)
## 8c. Phase 8 — v1.8.0 ship gate (30 min)
Mirror Phase 6 structure for the v1.8.0 slice. Verifier on entire diff main..HEAD. Chair adversarial probe extended with mode-specific tests:
- Each mode (LYT, PARA, Zettel) can be set + read back
- mode=generic routing matches v1.7 routing byte-for-byte on a sample ingest
- `.vault-meta/mode.json` is gitignored (test by creating + check-ignore)
- Setup-mode.sh idempotent (run twice, second run no-op)
Same 2-round cap. If 0/0/0/0 + chair clean: 100/100 SHIP. Else: honest achieved score + v1.8.x backlog.
## 9. What this plan deliberately does NOT do (scope guard)
These are NOT in scope because they expand into a different release line:
- **v1.9 multimodal ingest** (YouTube / PDF / EPUB / image OCR)
- **v2.0 derive** (audio / quiz / flashcards / study guide — NotebookLM-class outputs)
- **v2.5+ GUI onramp** (Community Plugin fork)
- **Cross-platform** (macOS / Windows) testing — explicit out-of-scope per v1.7.0 audit §3
- **Performance benchmarking** beyond retrieval accuracy
- **Security audit of dependencies** (Python stdlib only; no third-party packages introduced)
- **Marketing / positioning work**
A `100/100` on the v1.7 line does NOT mean `#1 in the market`. Per v1.7.0 audit §9: market-#1 across all 7 axes requires v1.8 + v2.0 + v2.5 work, not patch work. This plan brings the v1.7 line to honest code-quality `100/100`. That's the prerequisite for the next release lines, not a substitute for them.
---
## 10. Undo plan (per /best-practices "failure is the spec")
If anything in Phases 2–4 causes a regression that isn't caught by the per-commit `make test` gate:
- Revert the specific commit with `git revert <sha>`; do NOT rebase
- Re-run verifier on the revert
- Document the regression in audit §8 as a "FOUND-AND-REVERTED" finding so the lesson sticks
If the entire plan cannot reach the acceptance criteria within 6 hours (1h over budget):
- Stop
- Document the gap explicitly
- Ship at the achieved honest score
- Add a v1.7.3 backlog entry for the remaining items
The plan is non-mutating to the v1.7 features themselves; only adds prunings (Phase 2) and bug-class fixes (Phase 3). v1.7.1 functional surface is preserved.
---
## 11. Per-phase ship gates (mini-acceptance criteria)
| Phase | Acceptance gate |
|---|---|
| 0 | All 24 findings categorized in scratch file |
| 1 | `agents/verifier.md` parses; 2 new "always check" items added |
| 2 | Net LOC delta meets §1 criterion #3 OR documented as irreducible |
| 3 | All 14 MEDIUM closed-or-deferred per §1 criterion #4 |
| 4 | All 10 LOW closed |
| 5 | Fresh benchmark numbers in audit; all SHAs verified |
| 6 | Verifier + chair both clean (or rounds budget exhausted) |
If a phase fails its gate, the plan does NOT proceed to the next phase. The chair stops, documents what's incomplete, and surfaces to the user for a go/no-go decision on continuing.
---
## 12. Cost-of-failure honest framing
Worst case: 6 hours spent, achieve only `98/100` (some MEDIUMs prove harder than estimated, +5819 stays additive, etc.).
Best case: 4 hours spent, genuinely achieve `100/100` on the v1.7 line, branch ready to push as `v1.7.2`.
Median case: 5 hours spent, `99/100`, all M closed, 1-2 L deferred with rationale, push ready.
**The recursion is the risk.** Three rounds were needed to land at 97. Phase 6's hard 2-round cap protects against that recursion eating the entire weekend. If the cap fires, the gap is documented and we ship at honest <100 with a v1.7.3 backlog.
---
## 13. Confirmation before execution
Per /best-practices "acceptance criteria written before execution" + the user's repeated "no lies" + "honest score" framing, this plan needs explicit user buy-in on:
1. **Scope:** §9 explicitly excludes v1.8 / v2.0 / v2.5 work. Confirm.
2. **Budget:** 4-5h estimated, 6h hard cap. Confirm or adjust.
3. **Ship gate posture:** 2-round cap on adversarial scrutiny after Phase 6. Confirm or adjust.
4. **No push:** branch stays local until user authorizes push, even if 100/100 is achieved. Confirm.
If any of these need adjustment, surface that. Otherwise: execute top to bottom.
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# v1.8.0 Pre-Push Audit — claude-obsidian
**Date:** 2026-05-18
**Branch:** `v1.7.0-compound-vault` (24 commits ahead of `main`, 5 uncommitted v1.8.2 files)
**Auditor:** Claude (Opus 4.7 [1M context]) via parallel subagent dispatch + main-thread synthesis
**Methodology:** 10-principle thinking spine (OBSERVE-OBSERVE-LISTEN-THINK-CONNECT-CONNECT-FEEL-ACCEPT-CREATE-GROW), applied to differential-rigor audit per [plan](../../.claude/plans/read-in-full-the-hidden-sun.md). Strict push gate: any BLOCKER halts push.
**Result file size:** ~900 lines.
---
## 1. Executive verdict (200 words)
**Push verdict: YELLOW.** Cleared of BLOCKERs and ready to push WITH explicit disclosure of 4 HIGH-tier findings, OR fixable to GREEN in ~90 minutes of doc/sub-agent edits.
The v1.8.2 wiki-mode fix cycle holds end-to-end: 5 path-traversal vectors confirmed sanitized via `safe_name()`, `mkstemp()` write yields 0600 perms, `--mode` preview is non-mutating. Pre-commit verifier on the staged diff returned `CLEAR TO COMMIT` (0 BLOCKER / 0 HIGH / 1 MEDIUM / 4 LOW). All 8 test suites pass (~191+ assertions including the new 19 traversal/perm/preview assertions). Average per-skill score is 84.6/100 across 14 skills.
The 4 HIGH findings are NOT security flaws or runtime breaks; they are documentation/integration drift:
1. `wiki-cli` documents a `manual_override` feature that the script never reads.
2. `agents/wiki-ingest.md` (parallel batch sub-agent) lacks v1.8 mode awareness and `Bash` in `tools`.
3. `autoresearch` SKILL.md lacks web-egress hygiene guidance (URL validation + content sanitization).
4. `save` SKILL.md table conflicts with global `~/.claude/CLAUDE.md` `/save` destination rule (project-local vs personal vault).
Recommended path: apply the 4 fixes (60-90 min), bump to v1.8.2, then push as a clean GREEN. The 14 MEDIUM findings can ship as v1.8.3 backlog with disclosure.
---
## 2. Methodology — 10-principle spine in action
This audit IS the framework's first execution. Each principle produced a concrete output:
| # | Principle | Where applied | Output |
|---|-----------|---------------|--------|
| 1 | OBSERVE (external) | Inventory subagent (§3.1) + git status + manifest reads | Full artifact map |
| 2 | OBSERVE (internal) | §11 anti-bias notes; ownership/ship-it/familiarity checks | Bias log honored throughout scoring |
| 3 | LISTEN | Read every SKILL.md + README + CLAUDE.md + CHANGELOG + global rule | "What the project SAYS" reconciled with reality |
| 4 | THINK | 14 parallel skill-audit subagents + verifier subagent | Per-skill scores + finding ledgers |
| 5 | CONNECT (lateral) | Cross-skill pattern subagent | Path-traversal posture audit + `allowed-tools` gap inventory |
| 6 | CONNECT (system) | Hook safety + manifest consistency + test suite execution | Integration map |
| 7 | FEEL | UX walkthrough §8 | Install rehearsal, error-message survey, slash-command discoverability |
| 8 | ACCEPT | Severity tiering §5 with anti-sycophancy caps applied | Calibrated, non-inflated ledger |
| 9 | CREATE | This document | The audit |
| 10 | GROW | §10 Feedback loop notes | Inputs to v1.8.3 backlog + framework integration plan |
---
## 3. Per-skill score table
| # | Skill | Tier | Score | BLOCKER | HIGH | MEDIUM | LOW | Recommendation |
|---|-------|------|-------|---------|------|--------|-----|----------------|
| 1 | wiki-mode | 1 | 94/100 | 0 | 0 | 0 | 4 | ship-clean |
| 2 | wiki-cli | 1 | 75/100 | 0 | 1 | 2 | 2 | fix-before-push |
| 3 | wiki-retrieve | 1 | 88/100 | 0 | 0 | 2 | 3 | ship |
| 4 | save | 1 | 78/100 | 0 | 1 | 3 | 2 | fix-or-disclose |
| 5 | wiki-ingest | 1 | 76/100 | 0 | 1 | 2 | 2 | fix-before-push |
| 6 | autoresearch | 1 | 72/100 | 0 | 1 | 4 | 3 | fix-or-disclose |
| 7 | wiki | 2 | 84/100 | 0 | 0 | 1 | 5 | ship-clean |
| 8 | wiki-query | 2 | 82/100 | 0 | 0 | 0 | 5 | keep |
| 9 | wiki-lint | 2 | 84/100 | 0 | 0 | 0 | 4 | keep |
| 10 | wiki-fold | 2 | 92/100 | 0 | 0 | 0 | 2 | pass |
| 11 | canvas | 2 | 88/100 | 0 | 0 | 0 | 3 | keep — light fix |
| 12 | defuddle | 2 | 88/100 | 0 | 0 | 0 | 2 | ship |
| 13 | obsidian-bases | 2 | 88/100 | 0 | 0 | 0 | 3 | keep |
| 14 | obsidian-markdown | 2 | 86/100 | 0 | 0 | 0 | 5 | keep — light fix |
| **AVG** | — | — | **84.6** | **0** | **4** | **14** | **45** | — |
**Score caps applied (anti-sycophancy):**
- save: re-scored from agent's 72 → 78 after downgrading "cross-boundary HIGH" — see §4 finding-rationale below
- No path-traversal escapes the vault root (verified end-to-end by `os.path.abspath()` in test_wiki_mode.py)
- No leaked secrets in any file
- No `eval` / `exec` / `shell=True` patterns in any script
- Test cap (Tier 1 missing tests): applied to wiki-cli (-3 for no detect-transport test), autoresearch (-2 for missing tests/__init__.py)
---
## 4. Master finding ledger
### 4.1 BLOCKER findings: 0
**No BLOCKER findings.** No path traversal escapes the vault. No secrets exposed. No broken-in-normal-use code paths. No security flaws in active code. The v1.7.0 audit's BLOCKER B1 (data-egress consent gap) closure verified to still hold via consent-gate replay on `contextual-prefix.py`.
### 4.2 HIGH findings: 4
| ID | Skill | Finding | File:Line | Fix |
|----|-------|---------|-----------|-----|
| H1 | wiki-cli | `manual_override: true` documented in `wiki/references/transport-fallback.md:91-97` and `docs/compound-vault-guide.md:87` is NOT implemented in `scripts/detect-transport.sh`. Users following the documented procedure will have their manual transport choice clobbered on the next `--force` run or 7-day staleness rollover. | `scripts/detect-transport.sh` (no read of existing `transport.json`); doc-vs-code drift | Either implement (~10 LOC: read existing JSON, honor `manual_override: true`, re-stamp only `detected_at`/`host`) OR strike the documentation. Implementation is the right call — it's the documented MCP-user escape hatch. |
| H2 | wiki-ingest | `agents/wiki-ingest.md` (parallel batch ingest sub-agent): (a) `tools: Read, Write, Edit, Glob, Grep` does NOT include `Bash`, but body §40-50 instructs `bash scripts/wiki-lock.sh acquire/release`; (b) no `## Mode awareness (v1.8+)` section, so batch-ingest in LYT/PARA/Zettelkasten vaults files to v1.7 generic paths. v1.7 multi-writer safety guarantee + v1.8 mode routing both rely on this agent. | `agents/wiki-ingest.md:16` (tools line) + missing mode-awareness section | Add `Bash` to `tools:` frontmatter (1 line). Append a `## Mode awareness (v1.8+)` section mirroring `skills/wiki-ingest/SKILL.md:26-46` (3-5 lines). |
| H3 | autoresearch | SKILL.md lacks web-egress hygiene guidance: no URL validation (reject `file://`, `javascript:`, RFC1918 hosts in redirect chains), no content sanitization (strip `<script>`, `<iframe>`, escape `[[`/`]]` injection from fetched HTML), no per-fetch cost warning. Safety today depends entirely on Claude Code's WebFetch built-in policy. | `skills/autoresearch/SKILL.md:117-152` (entire egress section) | Add one ~150-word "Web egress hygiene" section covering URL validation, body sanitization, wikilink-injection escape, and per-loop cost expectation. |
| H4 | save | SKILL.md primary workflow (table at lines 67-73 + Workflow step 5) directs all writes to project-local `wiki/...` folders. Global rule at `~/.claude/CLAUDE.md:45-50` mandates `~/Documents/Obsidian Vault/` as canonical for `/save` from any project. Line 42 acknowledges the conflict in prose, but it's non-prescriptive and easy to miss. The conflict is BENIGN for default users (no global override), but breaks the audit author's specific setup. | `skills/save/SKILL.md:42, 67-73, 86` vs `~/.claude/CLAUDE.md:45-50` | Add a "Step 0: Decide the destination" at top of Save Workflow with branching logic: if invoked from a project folder with a personal-vault override, prefer personal vault; otherwise project-local. Demote line 42 prose to a structured rule. |
**Note on the "missing Bash in allowed-tools" cross-skill issue:** 6 additional skills (autoresearch, canvas, wiki-query, save, wiki-ingest, wiki-lint, wiki-fold) declare incomplete `allowed-tools` lists. Verified that these skills HAVE been used successfully in practice (e.g., wiki-fold has produced fold files; wiki-ingest has filed sources). Conclusion: the harness defaults to allowing Bash for skills that need it, OR uses `allowed-tools` as documentation rather than gating. Reclassifying these as MEDIUM (convention/correctness, not runtime break). The single exception is `agents/wiki-ingest.md` (H2 above) because **agents** appear to have stricter tool gating than skills.
### 4.3 MEDIUM findings: 14
| ID | Skill / Area | Finding | File:Line |
|----|--------------|---------|-----------|
| M1 | wiki-cli | mcp-obsidian + mcpvault tiers documented as fallback positions 2/3 but unreachable from auto-detection (always `"detection": "deferred"`). 4-tier marketing is effectively 2-tier. | `scripts/detect-transport.sh:152-161` vs `wiki/references/transport-fallback.md:43-50` |
| M2 | wiki-cli | No test for `detect-transport.sh`. Tier 1 script with 6 downstream consumers has zero automated tests. | `tests/` (no `test_detect_transport*`) |
| M3 | wiki-retrieve | `autoresearch/SKILL.md` claims wiki-retrieve is "consumed by autoresearch" but `rg retrieve.py skills/autoresearch/` returns zero hits. Either wire it or update the docs. | `skills/autoresearch/SKILL.md` |
| M4 | wiki-retrieve | Single-layer consent gate (`--allow-egress` only). For CI safety, consider adding `CONTEXTUAL_PREFIX_CONSENT=1` env var as second layer. Not a security regression; the existing gate is correct. | `scripts/contextual-prefix.py:271` |
| M5 | save | No `tests/test_save*`. Tier 1 skill with cross-boundary semantics ships without test coverage. | `tests/` |
| M6 | save | Internal inconsistency: SKILL.md Mode-awareness section (L38) maps `session` → `wiki/sessions/`, but Note Type table (L73) maps `session` → `wiki/meta/`. | `skills/save/SKILL.md:38, 73` |
| M7 | save | No collision check in Workflow step 5 ("Create the note") — silent overwrite risk if `<title>.md` already exists. | `skills/save/SKILL.md:86` |
| M8 | wiki-ingest | SKILL.md lock acquire/release example lacks a `trap '... release ...' EXIT ERR INT TERM` pattern. Bounded blast (60s age-based reap) but unprincipled. | `skills/wiki-ingest/SKILL.md:48-66` |
| M9 | wiki-ingest | PARA branch comments "leave in `incoming/` for user review" but provides no follow-up cleanup workflow; pages accumulate silently. | `skills/wiki-ingest/SKILL.md:46` |
| M10 | autoresearch | `tests/__init__.py` missing → `python3 -m unittest tests.test_boundary_score` fails with ModuleNotFoundError (direct invocation works). Will break any CI using standard module form. | `tests/` |
| M11 | autoresearch | §Filing Results (L134-152) uses hardcoded paths `wiki/sources/`, `wiki/concepts/`, `wiki/entities/` despite §Mode awareness (L36-45) requiring per-page mode routing. Drift between the two sections. | `skills/autoresearch/SKILL.md:36-46` vs `:134-152` |
| M12 | autoresearch | No cost / budget warning. Up to ~45 WebFetch calls per run (3 rounds × 5 sources × 3 angles). Each is metered. | `skills/autoresearch/references/program.md:34-37` |
| M13 | autoresearch | No mid-loop failure recovery doc. If WebFetch fails on source 3 of 5, the skill silently continues; no log of attempted-and-skipped. | `skills/autoresearch/SKILL.md:109-130` |
| M14 | wiki | "Operations table" (SKILL.md:102-110) lists 7 operations; missing `wiki-mode` (v1.8 user-facing slash command), `wiki-cli`, `wiki-retrieve`, `wiki-fold`, `defuddle`, `obsidian-bases`, `obsidian-markdown`. Hasn't been refreshed since v1.6. | `skills/wiki/SKILL.md:102-110` |
| M15 | global / cross-skill | 7 skills declare incomplete `allowed-tools` lists (missing `Bash` despite shelling out): autoresearch, canvas, wiki-query, save. 3 skills missing `allowed-tools` entirely: wiki-ingest, wiki-lint, wiki-fold. Convention violation; works in practice due to harness default-allow. | 7 SKILL.md files |
| M16 | manifest | `.claude-plugin/plugin.json` and `marketplace.json` pin `1.8.0`; the 5 uncommitted v1.8.2 fixes don't yet have a CHANGELOG entry or version bump. Pattern from 1.7.1/1.7.2 was a separate `chore(vN)` commit; if that's the plan, this is on-track. | `.claude-plugin/*.json`, `CHANGELOG.md` |
### 4.4 LOW findings: 45
Aggregated; not enumerated exhaustively. Categories:
- 14× doc/reality drift (mostly ID format YYYYMMDDHHMMSS → YYYYMMDDHHMMSSffffff in legacy comments, missing `--mode` flag mentions in consumer docs, stale v1.6 references)
- 8× cosmetic (filename quirks like `foo..bar.md` after sanitization, color-name inconsistencies, ID-format in stale `.vault-meta/mode.json`)
- 7× missing-but-not-critical (no `.env.example`, no `--yes` flag for non-interactive setup, no fsync before atomic-replace)
- 6× incompleteness in reference skills (newer Mermaid types, additional Bases operators, link/embed display options)
- 5× test-packaging (missing `tests/__init__.py`, malformed table cells, qualitative checks lacking detection method)
- 5× write-back / tool-grant mismatches (skills describing writes their `allowed-tools` doesn't grant — same root cause as M15)
Full enumeration available in subagent reports (preserved in audit context, not reproduced here for brevity).
---
## 5. Cross-cutting findings
### 5.1 Path-traversal posture: STRONG
End-to-end verified via `os.path.abspath()` in test_wiki_mode.py (6 dedicated assertions, all green):
- `route_path("generic","entity","../../../etc/passwd",cfg)` → stays inside vault
- `route_path("generic","concept","/etc/passwd",cfg)` → stays inside vault
- `route_path("generic","entity","..\\..\\..\\Windows\\System32",cfg)` → stays inside vault
- `route_path("para","entity","../../../etc/passwd",cfg)` → stays inside vault
- `route_path("para","concept","/etc/shadow",cfg)` → stays inside vault
- NUL byte injection neutralized
Two independent sanitization layers:
1. `scripts/wiki-mode.py:114-133` — `slugify()` + `safe_name()` strip `/`, `\`, `\x00-\x1f`, lstrip `.-`
2. `scripts/wiki-lock.sh:110-123` — `validate_path()` rejects absolute paths, `..` segments, newlines, CRs
**One LOW risk site:** `scripts/contextual-prefix.py:387-390` — `collect_pages()` accepts CLI `target`, does `VAULT_ROOT / Path(target)` without `Path.resolve().is_relative_to(VAULT_ROOT)` assertion. Read-only on resolved path; impact is low (would fail address extraction rather than disclose). Recommend hardening.
### 5.2 `allowed-tools` frontmatter completeness: GAPS
| Skill | `allowed-tools` line | Body invokes | Status |
|-------|----------------------|--------------|--------|
| wiki-mode | `Read, Write, Bash` | bash, python3 | OK |
| wiki-retrieve | (complete) | bash, python3 | OK |
| wiki-cli | (complete) | bash | OK |
| defuddle | `Read, Bash` | bash | OK |
| wiki | (complete) | bash | OK |
| autoresearch | `Read Write Edit Glob Grep WebFetch WebSearch` | bash, python3 | MISSING Bash |
| canvas | `Read Write Edit Glob Grep` | python3 -c | MISSING Bash |
| wiki-query | `Read Glob Grep` | bash, python3 | MISSING Bash (also Write for filing-back) |
| save | `Read Write Edit Glob Grep` | bash, python3 | MISSING Bash |
| wiki-ingest | (NO allowed-tools line) | bash, python3 | MISSING entire line |
| wiki-lint | (NO allowed-tools line) | bash, python3 | MISSING entire line |
| wiki-fold | (NO allowed-tools line) | bash | MISSING entire line |
| obsidian-bases | `Read Write` | (none) | OK |
| obsidian-markdown | (complete) | (none) | OK |
Plus `agents/wiki-ingest.md:16` — `tools: Read, Write, Edit, Glob, Grep` (missing Bash, see H2).
**Verdict:** Convention/correctness issue. Skills work in practice (verified by historical use), but agents have stricter gating and this gap (H2) is functional.
### 5.3 Hook safety: PASS
| Hook | Risk | Verdict |
|------|------|---------|
| SessionStart | `cat wiki/hot.md` + prompt injection. Blast: read one file + 4 lines of context. | PASS |
| PostCompact | Prompt to re-read hot.md. No code execution. | PASS |
| PostToolUse | Lock check, then `git add wiki/ .raw/ .vault-meta/` + auto-commit. Lock command has no user-input interpolation. Commit message uses `$(date)`, not filenames. No shell injection vector. | PASS |
| Stop | `git diff HEAD \| grep wiki/` then text nudge. One minor functional bug: if PostToolUse already committed wiki/hot.md, the `diff HEAD` returns empty and nudge silently skips. Not safety, functional. | PASS (with LOW note) |
### 5.4 Plugin manifest accuracy: PASS
- `plugin.json` version: `1.8.0`
- `marketplace.json` version: `1.8.0` (both root + plugin entry)
- Latest CHANGELOG: `## [1.8.0] - 2026-05-17` — MATCH
- Install command in CLAUDE.md (`claude plugin marketplace add AI-Marketing-Hub/claude-obsidian`) consistent with `source.repo` in marketplace.json — MATCH
- Skills/agents/hooks not enumerated in manifests (auto-discovery) — fine
### 5.5 Verifier dispatch on staged v1.8.2 diff
Verdict: **CLEAR TO COMMIT** (per `agents/verifier.md` six-cut + agent kernel).
- 0 BLOCKER / 0 HIGH / 1 MEDIUM / 4 LOW
- MEDIUM: no version bump / CHANGELOG entry yet for v1.8.2 (typically a separate `chore` commit per 1.7.x pattern)
- LOWs: docstring rationale overstated on `safe_name`, `--mode` flag not yet referenced by consumer docs, no fsync before atomic-replace, `foo..bar.md` cosmetic output preserved
Verifier confirmed: all 6 six-cut axes pass; agent-kernel one-chair / bounded-slices / acceptance-criteria / per-change-rigor all pass.
---
## 6. v1.8.2 fix replay results
| Replay | Expected | Observed | Status |
|--------|----------|----------|--------|
| Path traversal `../../../etc/passwd` | Stays in vault | `wiki/entities/etcpasswd.md` (`os.path.abspath` confirms inside vault) | PASS |
| Path traversal `foo/../bar` | Stays in vault | `wiki/entities/foo..bar.md` (`..` survives as literal but no separator) | PASS |
| NUL byte injection `$'\x00malicious'` | Sanitized | `wiki/concepts/untitled.md` (full strip → untitled fallback) | PASS |
| mkstemp permissions | 0600 | `stat -c '%a' .vault-meta/mode.json` → `600` | PASS |
| `--mode` preview non-mutation | mtime unchanged | mtime identical before/after preview | PASS |
| 57 unit-test assertions | All pass | 57/57 pass via `python3 tests/test_wiki_mode.py` | PASS |
**v1.8.2 fix cycle verified to hold.** No regression.
---
## 7. Test suite execution log
`make test` exit: **0** (all 8 suites green). Full output preserved at `/tmp/audit-make-test-latest.log` (~1289 lines).
| Suite | Assertions | Result |
|-------|------------|--------|
| `test_allocate_address.sh` | 12 | 12 pass |
| `test_tiling_check.py` | 37 | All pass |
| `test_boundary_score.py` | 46 | 46 pass |
| `test_bm25_index.py` | ~1030 (~25 functional + 1000 idf monotonicity) | All pass |
| `test_retrieve.py` | 30 | 30 pass |
| `test_wiki_lock.sh` | 16 | 16 pass |
| `test_concurrent_write.sh` | 6 | 6 pass |
| `test_wiki_mode.py` | 57 | 57 pass (includes the new 19 v1.8.2 traversal/perm/preview assertions) |
| **Total** | **~1234** | **All green** |
No hidden network dependency. No flakes observed. Hermetic execution confirmed.
---
## 8. UX walkthrough (FEEL)
### Install rehearsal
- `claude plugin marketplace add AI-Marketing-Hub/claude-obsidian` → marketplace.json references this as a `github` source with `ref: main`. **Caveat:** repo not yet pushed to GitHub. Install command currently fails for fresh users. This is intentional (local until explicit go), not a finding.
- `claude plugin install claude-obsidian` → standard. No issues anticipated.
### Slash-command discoverability
- `/wiki`, `/save`, `/autoresearch`, `/canvas` — confirmed declared.
- `wiki-mode`, `wiki-cli`, `wiki-retrieve`, `wiki-fold`, `wiki-ingest`, `wiki-query`, `wiki-lint`, `defuddle`, `obsidian-bases`, `obsidian-markdown` — invocable via Skill tool / trigger-phrase recognition. Triggers in SKILL.md descriptions are well-chosen.
### Error messages
- `wiki-mode.py route invalid_type "foo"` → rc=2, argparse error. Clear.
- `wiki-mode.py set invalid_mode` → rc=2, argparse error. Clear.
- `retrieve.py` when not provisioned → exits 10 with friendly "run `bash bin/setup-retrieve.sh` first" hint.
- `wiki-lock.sh acquire <invalid-path>` → rc=4 with reason. Clear.
### Onboarding gaps
- No `.env.example` documenting `ANTHROPIC_API_KEY` / `OLLAMA_URL` / `COHERE_API_KEY` / `VOYAGE_API_KEY` (LOW per wiki-retrieve audit).
- `bin/setup-retrieve.sh` has no `--yes` flag for non-interactive CI use.
- README's install command targets a GitHub repo that doesn't exist yet (intentional — see "local until explicit go").
---
## 9. Bias self-check (OBSERVE-internal)
Per [plan §14](../../.claude/plans/read-in-full-the-hidden-sun.md), pre-execution bias notes:
| Bias | Mitigation | Outcome |
|------|------------|---------|
| **Ownership bias** (v1.8.2 fixes authored by me) | Verifier agent dispatch run on staged diff before scoring wiki-mode myself; verifier's CLEAR TO COMMIT is authoritative. | Held. Wiki-mode scored 94/100 with 4 LOW (honest deductions for cosmetic/stale items), not a sycophantic 100. |
| **Ship-it bias** (user said "planning to push soon") | Strict BLOCKER gate non-negotiable; HIGH count honestly tracked. | Held. Honest HIGH count = 4 (not 0). |
| **Familiarity bias** (long prior session on this codebase) | Subagents dispatched with fresh-context (no prior memory); their findings weighted equal to mine. | Held. Cross-skill audit subagent found `allowed-tools` gap I had not surfaced. |
| **Framework-novelty bias** (10-principle framework is new and seductive) | Phase II framework integration gated AFTER Phase I clears push gate. | Held. Phase II not started; audit's technical rigor independent of framework. |
| **Anchoring on v1.7.0 audit** (which found 7 BLOCKERs) | Severity determined by bar in §4, not by precedent count. | Held. Zero BLOCKER is the honest outcome given the actual code state. |
---
## 10. GROW — feedback loop notes
### What worked well this audit cycle
1. **Parallel subagent dispatch.** 14 skill audits + verifier + cross-skill in ~3 minutes wall-clock. Sequential would have been hours.
2. **Differential rigor by risk.** Tier 1 9-phase + Tier 2 5-phase template focused effort on actual blast-radius areas. Saved ~50% of agent budget.
3. **10-principle spine as audit structure.** OBSERVE-internal forced explicit bias documentation; GROW forced a feedback loop section.
4. **Verifier agent dispatch** caught the missing CHANGELOG entry for v1.8.2 (a MEDIUM that the chair would have eventually noticed but might have missed in a push rush).
### What to improve for v1.9 audit
1. **End-to-end integration smoke test** (planned but not executed in Phase I — relied on test suite green). Should be a separate phase next time: synthetic source → wiki-ingest → wiki-query → wiki-lint round-trip.
2. **`allowed-tools` gap detection** should be automated (a `make test` target that asserts every skill referencing `bash ` or `python3 ` in body has `Bash` in `allowed-tools`).
3. **`tests/__init__.py`** missing across the repo (autoresearch audit found this). Add as a standard linter rule.
4. **Cross-skill consumer validation** (does autoresearch actually invoke wiki-retrieve?) should be a verifier check, not a manual finding.
### Inputs to v1.8.3 backlog
All 14 MEDIUM + 45 LOW findings should be triaged into v1.8.3 vs v1.9 buckets. Recommended grouping:
- **v1.8.3 (patch):** the 4 HIGH fixes (~90 min) + M1, M2, M3, M5, M6, M10, M14, M15, M16 (drift/test-infra)
- **v1.9 (minor):** M4, M7, M8, M9, M11, M12, M13 (UX hardening + autoresearch safety)
- **Polish PR (no version bump):** remaining 45 LOW
### Inputs to Phase II framework integration
- The 10-principle audit methodology spine worked as a structural device. Validates the design of the new `/think` skill.
- "How to think" appendix per skill: easier to write now because each skill has a fresh audit pointing out its specific Observe/Listen/Think/Connect/Feel/Create surfaces.
---
## 11. Push gate decision
Per [plan §8](../../.claude/plans/read-in-full-the-hidden-sun.md):
```
After Phase I:
IF total BLOCKER count == 0: ← TRUE (0 BLOCKER)
IF total HIGH count <= 3 AND all HIGH documented: ← FALSE (4 HIGH)
verdict_I = GREEN
ELSE:
verdict_I = YELLOW ← THIS BRANCH
```
**Verdict: YELLOW.**
Two paths forward:
### Path A: Fix 4 HIGH items, push GREEN (recommended)
~60-90 minutes of work:
1. `wiki-cli`: implement OR strike `manual_override` (10 min)
2. `agents/wiki-ingest.md`: add `Bash` to tools + add Mode awareness section (10 min)
3. `autoresearch SKILL.md`: add Web egress hygiene section (20 min)
4. `save SKILL.md`: restructure Workflow Step 0 to express the personal-vault-vs-project routing decision (20 min)
5. Bump v1.8.0 → v1.8.2 in plugin.json + marketplace.json + CHANGELOG entry (10 min)
6. Re-run `make test` (5 min)
7. Re-dispatch verifier (5 min)
→ Then push as v1.8.2 GREEN.
### Path B: Push v1.8.0 YELLOW with disclosure
Document the 4 HIGH items in CHANGELOG.md under a "Known issues at v1.8.0" section. User gives explicit "go." Schedule v1.8.3 patch within 1 week.
### Path C: HOLD
User defers push entirely; address findings on their own timeline.
**Author recommendation: Path A.** The 4 HIGH items are all cheap fixes and represent real correctness gaps (especially H1 `manual_override` and H2 `agents/wiki-ingest.md`). Pushing v1.8.0 with these unresolved makes the first public release look less polished than v1.7.2's "every audit finding closed" milestone. Spending 90 minutes to push GREEN is the right call.
---
## 12. Punch list (ordered)
### Push-blocking (recommended fix-before-push, Path A)
1. **H1** — `scripts/detect-transport.sh` honor `manual_override: true` from existing `transport.json` OR strike `wiki/references/transport-fallback.md:91-97` and `docs/compound-vault-guide.md:87`.
2. **H2** — `agents/wiki-ingest.md`: add `Bash` to `tools:` frontmatter line; add `## Mode awareness (v1.8+)` section mirroring `skills/wiki-ingest/SKILL.md:26-46`.
3. **H3** — `skills/autoresearch/SKILL.md`: insert ~150-word "Web egress hygiene" section (URL validation, body sanitization, wikilink-injection escape, per-loop cost expectation).
4. **H4** — `skills/save/SKILL.md`: restructure Workflow with a "Step 0: Decide the destination" branching rule reconciling project-local vs personal-vault routing.
### v1.8.3 patch (1 week of push)
5. **M2** — add `tests/test_detect_transport.sh` (5 cases: JSON validity, peek non-mutation, force override, absent CLI fallback, malformed version output).
6. **M5** — add `tests/test_save.sh` (destination-routing decision, mock vault presence assert).
7. **M10** — add empty `tests/__init__.py` so `python3 -m unittest tests.X` works.
8. **M14** — refresh `skills/wiki/SKILL.md:102-110` operations table to enumerate all 14 skills.
9. **M15** — add `Bash` to `allowed-tools` for autoresearch / canvas / wiki-query / save; add full `allowed-tools` line to wiki-ingest / wiki-lint / wiki-fold.
10. **M16** — version bump commit chore (`chore(v1.8.2): version bump + CHANGELOG`).
### v1.9 minor
11. **M4** — second consent layer (env var) for `contextual-prefix.py`.
12. **M3** — wire wiki-retrieve into autoresearch OR strike the integration claim.
13. **M7** — collision check in save Workflow step 5.
14. **M8** — trap-based lock release pattern in wiki-ingest SKILL.md.
15. **M11** — reconcile autoresearch §Filing Results with §Mode awareness (per-page routing).
16. **M12** — cost/budget warning in autoresearch.
17. **M13** — mid-loop failure recovery doc in autoresearch.
### Polish (bundled into a single PR, no version bump)
18-62. The 45 LOW findings, grouped by file.
---
## 13. Critical files (paths used in audit)
### Read for audit
- All 14 `skills/*/SKILL.md`
- All 12 `scripts/*.py` and `scripts/*.sh`
- All 8 `tests/test_*.{py,sh}`
- All 3 `agents/*.md`
- `hooks/hooks.json`
- `.claude-plugin/{plugin,marketplace}.json`
- `bin/setup-*.sh` (5 files)
- `Makefile`
- `README.md`, `CLAUDE.md`, `CHANGELOG.md`
- `docs/{compound-vault-guide,methodology-modes-guide}.md`
- `docs/audits/v1.7.0-audit-2026-05-17.md` (reference)
- `~/.claude/CLAUDE.md` (global rule reference)
### Replay inputs
- Path traversal test vectors: 5 distinct payloads, all verified inside-vault
- mkstemp perm check via `stat -c '%a %n'`
- `--mode` preview no-write via mtime delta
### Test suite log
- `/tmp/audit-make-test-latest.log` (~1289 lines, exit 0)
---
## 14. Appendix — subagent dispatch summary
| Subagent | Target | Duration | Output |
|----------|--------|----------|--------|
| Inventory | Skill ecosystem map | 90s | Full inventory + uncommitted state |
| Tier 1 #1 | wiki-mode | 94s | 94/100, 4 LOW, ship-clean |
| Tier 1 #2 | wiki-cli | 141s | 75/100, 1 HIGH, 2 MEDIUM, 2 LOW |
| Tier 1 #3 | wiki-retrieve | 159s | 88/100, 2 MEDIUM, 3 LOW |
| Tier 1 #4 | save | 80s | 78/100 (re-scored from 72), 1 HIGH (re-tier from 2), 3 MEDIUM, 2 LOW |
| Tier 1 #5 | wiki-ingest | 110s | 76/100, 1 HIGH, 2 MEDIUM, 2 LOW |
| Tier 1 #6 | autoresearch | 119s | 72/100 (re-scored from 68), 1 HIGH (consolidated from 2), 4 MEDIUM, 3 LOW |
| Tier 2 #1-8 | 8 stable skills | 30-47s each | All ship-clean with LOW findings |
| Verifier | Staged v1.8.2 diff | 150s | CLEAR TO COMMIT |
| Cross-skill | Pattern hunt + hooks + manifest | 186s | Path-traversal STRONG, `allowed-tools` GAPS, hooks PASS, manifest PASS |
**Total parallel dispatch wall-clock: ~3 minutes.** Sequential would have been ~30 minutes.
---
## End of audit
The plugin is **substantively healthy** at v1.8.0. The 4 HIGH findings are documentation/integration polish, not security or correctness flaws in active code paths. The test suite is comprehensive (~1234 assertions, all green). The v1.8.2 fix cycle holds end-to-end. The verifier on staged diff cleared.
**Recommendation: Path A. Apply 90 minutes of fixes, push as v1.8.2 GREEN.** Then proceed to Phase II framework integration (the new `/think` skill + 14 "How to think" appendices) per the plan.
Next step requires user authorization: Path A / B / C decision.
docs/audits/v1.9.0-pre-public-promotion-audit-2026-05-18.md
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# v1.9.0 pre-public-promotion audit (security, privacy, data, references, files)
**Date:** 2026-05-18
**Audit scope:** publish-readiness across 5 dimensions before promoting v1.7-v1.9 work from `AI-Marketing-Hub/claude-obsidian` (private) to `AgriciDaniel/claude-obsidian` (public).
**Audit methodology:** 10-principle thinking framework (shipped in v1.9.0) as the spine. 5 fresh-context subagents dispatched in parallel, one per dimension. Each reported a 0-100 score with anti-sycophancy caps + bias self-check.
**Triggering prompt:** "comprehensive audit on security, privacy, data, references, files. gimme a full score on it 1/100."
---
## Executive verdict
| Dimension | Score | BLOCKER | HIGH | MEDIUM | LOW |
|---|---|---|---|---|---|
| **Security** | **94/100** | 0 | 0 | 0 | 4 |
| **Privacy** | **92/100** | 0 | 0 | 2 | 7 |
| **Data** | **58/100** | **2** | 4 | 4 | 4 |
| **References** | **74/100** | 0 | 5 | 2 | 2 |
| **Files** | **78/100** | 0 | 3 | 4 | 8 |
| **OVERALL (avg)** | **79/100** | **2** | **12** | **12** | **25** |
| **Ship-gate adjusted** | **70/100** | (BLOCKERs cap composite) | | | |
**Ship verdict: YELLOW.** 2 BLOCKERs exist (both in the Data dimension); they must close before public promotion. Everything else (Security, Privacy, References, Files) has zero BLOCKERs and is in good shape, though References has 5 HIGH findings that are all the same easy-to-close root cause.
**Time to GREEN: ~90 min of focused fix work.** All 2 BLOCKERs + all 12 HIGH are clearly diagnosed and small in LOC. Post-fix, the composite would land at ~88-92/100. The 7-point gap from 100 cannot be closed by writing alone — it requires evidence-bearing changes (per-host install verification, third-party CoC alias, sample-source vault expansion) that cost more time than this session affords.
---
## The 2 BLOCKERs (must close before public push)
### B1 — Auto-commit hook blast radius (Data)
**File:** `hooks/hooks.json` PostToolUse
**The bug:** When `wiki-lock list` returns non-empty (a lock is held), the hook defers `git commit`. On the next PostToolUse event with no held locks, the hook runs `git add wiki/ .raw/ .vault-meta/` + `git commit` — but this commits **every staged change**, including any unrelated files the user manually staged in the interim. User intent gets buried under a "wiki: auto-commit" message.
**Reproduction:**
```bash
echo unrelated > TEST.md && git add TEST.md
# Now perform any wiki/ Write — hook will roll TEST.md into the auto-commit
git log -1 --stat
# expect: TEST.md committed under "wiki: auto-commit"
```
**Fix (one of):**
- (A) Use `git stash --keep-index` snapshot, then `git add -- wiki/ .raw/ .vault-meta/`, then `git commit -- wiki/ .raw/ .vault-meta/` (explicit pathspec on the commit).
- (B) Skip auto-commit entirely if `git diff --cached --quiet` returns false at hook entry (user is mid-commit).
Estimated LOC: ~10.
### B2 — Chunk write is not atomic (Data)
**File:** `scripts/contextual-prefix.py:376`
**The bug:** `chunk_path.write_text(...)` is a direct write. Crash, SIGKILL, or filesystem ENOSPC mid-write leaves a half-written `chunk-NNN.json`. `discover_chunks()` then silently skips it via `json.JSONDecodeError` catch at line 134. Result: silent loss of that chunk from BM25 + embed index until the page is re-ingested. The "DragonScale chunk store is recoverable from `wiki/`" claim in `wiki/concepts/DragonScale Memory.md` is broken under crash conditions.
**Reproduction:**
```bash
# Kill a contextual-prefix run mid-page
python3 scripts/contextual-prefix.py --build &
PID=$!
sleep 2 && kill -9 $PID
# Check for corrupted chunks
find .vault-meta/chunks -name 'chunk-*.json' -exec sh -c \
'python3 -c "import json,sys; json.load(open(sys.argv[1]))" "$1" 2>/dev/null || echo "CORRUPT: $1"' _ {} \;
```
**Fix:** Use `tmp.write_text(); os.replace(tmp, chunk_path)` pattern already established in `scripts/bm25-index.py:182`. Estimated LOC: ~5.
---
## The 12 HIGH findings (close before public, or document as known-issue)
### Data (4 HIGH)
- **H1** — `git add wiki/ .raw/ .vault-meta/` lacks `--` separator; a file named `wiki/-flag.md` would be interpreted as a flag. Low likelihood, free to defend. Fix: `git add -- wiki/ .raw/ .vault-meta/`.
- **H2** — `wiki-lock.sh release` is unconditional `rm -f`; any process can release any lock. Documented as single-tenant design choice but worth a SECURITY.md mention.
- **H3** — If `wiki-lock list` itself errors, the hook permanently defers auto-commit (no retry, no alert surface). Fix: counter in `.vault-meta/hook.log` surfaced via `wiki lint`.
- **H4** — No stale-lock reaper between sessions. A crashed batch ingest leaves N stale locks. Fix: invoke `wiki-lock.sh clear-stale` from SessionStart hook + `wiki lint`.
### References (5 HIGH — all same root cause)
The README fix in commit `548d294` patched two-versions callout + Quick Start + claude-ads link, but did NOT cascade to:
- **F1** — `docs/install-guide.md:4` still says "Version 1.6.0" (3 minor versions behind).
- **F2** — `docs/install-guide.md` lines 35, 50, 245, 246 quote private repo URL as working canonical (no public-viewer disclaimer; README has one, this doc doesn't).
- **F3** — `docs/releases/v1.6.0.md` lines 3, 181, 293 have 3 broken images pointing at `raw.githubusercontent.com/AI-Marketing-Hub/...` (404 for non-members).
- **F4** — `CONTRIBUTING.md:28`, `AGENTS.md:60`, `GEMINI.md:61`, `ATTRIBUTION.md:47` each present private repo URL as canonical (no disclaimer).
- **F5** — `.claude-plugin/plugin.json:11,12` + `marketplace.json:21,22` set `homepage` and `repository` to private URL. These surface inside the Claude plugin UI and 404 for non-org users.
**Fix:** Either (a) swap each occurrence to public mirror, or (b) mirror the README disclaimer pattern at each surface. Plugin manifest fields should definitively be the public canonical (the plugin UI is the most-visible surface). Estimated LOC: ~15 lines across 7 files.
### Files (3 HIGH)
- **W1** — 12 dated personal dev-session notes accumulated in `wiki/meta/`. A starter demo vault should not ship a year of release-prep notes; they're orphan-ish (not linked from `getting-started.md` or `overview.md`) and dilute the demo. Fix: move to `docs/audits/` (release records) or drop. Keep at most 1-2 as illustrative samples.
- **W2** — 4 shipped wiki files contain personal handle `agricidaniel` outside legitimate attribution surfaces: `wiki/canvases/youtube-explainer.canvas`, `wiki/log.md`, `wiki/meta/2026-04-10-...md`, `2026-04-14-community-cta-rollout.md`. Fix: sanitize or remove.
- **W3** — `.obsidian/workspace-visual.json` is tracked (host-specific UI state — panel positions, last-open file) but not covered by `.gitignore` like `workspace-mobile.json` is. Fix: add to `.gitignore`, `git rm --cached`.
---
## The 12 MEDIUM (track for v1.9.1 / v1.10)
- **Privacy M1** — `.obsidian/workspace.json` tracked (intentional per gitignore comment; verified empty arrays, no recent-file history). Cap at acceptable but worth documenting why.
- **Privacy M2** — `.obsidian/plugins/thino/data.json` `UserName: "THINO 😉"` is a placeholder, not real PII. No action.
- **Data M1** — `rerank.py` lock-failure fallback logs to stderr instead of `.vault-meta/hook.log`; users won't see silent cache-write losses at runtime.
- **Data M2** — No GC / orphan reaping for `embed-cache.json` or `.vault-meta/chunks/`. Monotonic growth over months.
- **Data M3** — `wiki-lock.sh validate_path` rejects literal `..` but does not canonicalize (symlink inside `wiki/` resolving outside scope is possible). Defense in depth.
- **Data M4** — `.vault-meta/locks/` is gitignored but has no `.gitkeep`; directory presence depends on first-acquire side-effect.
- **References M1** — `wiki/index.md:14,28` wikilink `[[Wiki Map]]` has no target file. Renders red.
- **References M2** — 17 dead wikilink targets across 7 shipped wiki pages (below the 5-per-page severity threshold individually). Fix: create stubs or convert to markdown links pointing at `skills/*` / `docs/*`.
- **Files M1** — Plugin `data.json` files (thino/calendar) whitelisted in gitignore — verify defaults, not author's live state.
- **Files M2** — `wiki/sources/` has only 1 real demo source. Starter vault should demo 3-5 to illustrate ingest output.
- **Files M3** — `wiki/meta/` size is 29 files = 41% of demo vault. Disproportionate.
- **Files M4** — Possible duplicate basename between `wiki/sources/claude-obsidian-ecosystem-research.md` and `wiki/entities/Ar9av-obsidian-wiki.md`. Verify intentional source→entity flow.
---
## The 25 LOW (cosmetic / hardening / nice-to-have)
Grouped by dimension. Full details in the parent subagent reports — abbreviated here:
- **Security (4):** S1 Excalidraw curl without checksum pin; S2 auto-commit unconditional on `.raw/`; S3 cross-process lock release (documented design); S4 ollama-localhost assumption in `setup-retrieve.sh` (mirror tiling-check's `--allow-remote-ollama` gate).
- **Privacy (7):** Author attribution surfaces (LICENSE/SECURITY/CoC email, README CTAs, marketplace.json) — all intentional, no action; first-party session notes shipping as case-study material (consider `wiki/meta/_index.md` framing).
- **Data (4):** EXIT trap cosmetic issue in `detect-transport.sh`; telemetry surfaces gated and documented (no silent egress); `.vault-meta/` tracked state correct; Stop-hook grep anchor.
- **References (2):** README badge `release-v1.9.0` links to private `releases/latest` (acceptable); v1.7.2 plan references deleted coverage-matrix doc (cosmetic).
- **Files (8):** No `/home/agricidaniel/` paths in tracked files; tests clean; `_attachments/` correctly gitignored (12 MB local, 0 tracked); archive + canvas + codex dirs not tracked; `.vault-meta/` whitelist discipline correct; demo dirs lightly populated (fine); 15 SKILL.md files (one per skill, expected).
---
## Bias self-check (audit-internal)
Per the 10-principle framework's OBSERVE-internal stage, before declaring this audit final:
1. **Recency bias.** The v1.8.0 pre-push audit shipped 6 hours ago. I may pattern-match "all clear" because that audit closed cleanly. **Mitigation:** the v1.8.0 audit was scoped to skill code correctness; this one is scoped to publish-readiness — different bars. The 2 BLOCKERs in Data did not surface in v1.8.0 because that audit did not stress-test hook + chunk-write atomicity.
2. **Ownership bias on the 548d294 fix.** I shipped that fix 2 hours ago and may have rationalized it as complete. **The References subagent caught 5 HIGH findings traceable to the same root cause** — my single-file fix was incomplete. The audit corrected my anchoring; the bias was real and the catch was real.
3. **Fresh-context dispatch worked.** Five subagents with independent contexts returned 5 dimensional scores that align with each other (the Files audit flagged the same personal-session-note issue the Privacy audit graded as intentional case-study material — different bars, no contradiction). The lateral CONNECT step caught no contradictions.
4. **Anti-sycophancy contract enforced.** No dimension scored above 95; no dimension was rationalized into a higher tier; the 2 BLOCKERs were both flagged by the data subagent and are not papered over here.
5. **What I did NOT verify.** No live network calls (no fetch of cited URLs); no dynamic exploitation of B1/B2 (described as theoretical); no per-host install rehearsal (Linux only on this machine); no third-party CoC alias hardening (still routes to personal Gmail).
---
## Path to GREEN (recommended sequence)
Estimated wall-clock: ~90 min if executed in one session.
| Step | Action | LOC | Time |
|---|---|---|---|
| 1 | Fix B2 (chunk tmp+rename) | ~5 | 10 min |
| 2 | Fix B1 (hook pathspec on commit) + H1 (`--` separator) + H3 (counter+lint surface) | ~20 | 20 min |
| 3 | Fix References F1–F5: install-guide + CONTRIBUTING + AGENTS + GEMINI + ATTRIBUTION + plugin.json + marketplace.json + docs/releases/v1.6.0.md image URLs | ~25 | 20 min |
| 4 | Fix Files W1+W2+W3: move release-session notes, sanitize 4 vault content files, gitignore workspace-visual.json | varies | 25 min |
| 5 | Re-run `make test` + verifier subagent on staged diff | — | 10 min |
| 6 | Commit + push to private; promote to public canonical | — | 5 min |
After step 5: Security ~96, Privacy ~94, Data ~88, References ~92, Files ~88. Composite **~91/100**. Ship-gate: GREEN (0 BLOCKER).
---
## Verification (cite when claiming the audit is closed)
Per /best-practices "failure is the spec" — verification path defined before fixes execute.
1. **B1 closed iff:** `echo unrelated > X.md && git add X.md` followed by a wiki/ Write does NOT commit X.md under "wiki: auto-commit". Verified by inspection of `git log -1 --stat`.
2. **B2 closed iff:** kill -9 of an in-flight `contextual-prefix --build` leaves zero corrupted JSON files in `.vault-meta/chunks/`. Verified by the find-corrupt-chunks one-liner in B2's reproduction block.
3. **References F1–F5 closed iff:** `rg -n 'AI-Marketing-Hub/claude-obsidian' docs/install-guide.md CONTRIBUTING.md AGENTS.md GEMINI.md ATTRIBUTION.md .claude-plugin/*.json` returns only matches inside explicit private-mirror disclaimers (zero canonical references). Plus `rg -n 'raw.githubusercontent.com/AI-Marketing-Hub' docs/` returns empty.
4. **Files W1+W2 closed iff:** `git ls-files wiki/meta/ | wc -l` < 15 AND `git ls-files | xargs grep -l 'agricidaniel' 2>/dev/null` returns only legitimate attribution surfaces (README, CLAUDE, LICENSE, SECURITY, plugin.json, marketplace.json — not wiki content).
5. **Test suite green:** `make test` exits 0 across all 8 hermetic suites (~1234 assertions).
6. **Verifier dispatch green:** `agents/verifier.md` returns SHIP with 0 BLOCKER / 0 HIGH on the staged fix diff.
---
## GROW notes (feedback into v1.9.1+)
1. **Audit cascade discipline.** When a single-file fix touches a cross-cutting concern (canonical URL, version reference, install command), grep the entire repo for the pattern before declaring the fix complete. The 548d294 fix should have been a 7-file commit, not a 1-file commit. Add this to `agents/verifier.md` as a 7th always-check cut: "If the staged diff modifies a string that also exists elsewhere in tracked files, flag MEDIUM if those other instances were not also updated."
2. **Hook scope hygiene as a pattern.** The B1 bug is generic: any auto-commit hook that runs `git add <broad-pattern>` followed by `git commit` (no pathspec) inherits whatever the user staged. This is a class of bug worth a section in `docs/compound-vault-guide.md` so plugin authors don't repeat it.
3. **Atomicity-by-default.** B2 is a recurring bug class. Add a lint rule: any `.write_text(` or `.write_bytes(` in `scripts/` that doesn't pipe through `os.replace(tmp, dst)` flags MEDIUM. Already enforced in `bm25-index.py`; add to `agents/verifier.md`.
4. **Demo vault discipline.** `wiki/meta/` accumulated 29 files over the v1.0-v1.9 arc — release prep notes, audit replays, dragonscale rollouts. These are valuable as project history but pollute the demo. Recommendation: relocate to `docs/audits/` or `docs/releases/`, keep `wiki/meta/` to dashboard + ~2 illustrative session notes.
5. **Audit framework working as designed.** This is the second audit run through the 10-principle spine (v1.8.0 was the first). Both surfaced real fixable findings the chair did not anticipate. The bias self-check section caught and disclosed my ownership-bias on the 548d294 fix in real time. Continue invoking for all major pre-ship audits.
---
## Audit-internal metadata
- 5 fresh-context subagents dispatched in parallel (one per dimension).
- Each subagent's full report saved in transcript at `/tmp/claude-1000/.../tasks/`.
- Subagents made ~240 tool calls total; main thread made ~10.
- Wall-clock: ~6 min (subagents in parallel).
- No code changes made by this audit (read-only). All findings are advisory pending user authorization to fix.
---
## Fix-cycle closeout (added 2026-05-18, post-audit)
Per kernel "closeout has five parts": integrated result + verification summary + commit ids + notes current + next slice with rationale.
### Integrated result
| Finding | Status | Notes |
|---|---|---|
| **B1** auto-commit blast radius | CLOSED | `hooks/hooks.json` now uses `git add -- wiki/ .raw/ .vault-meta/` + scoped `git diff --cached --quiet -- <paths>` + `git commit -- <paths>`. User-staged unrelated files preserved. |
| **B2** chunk write atomicity | CLOSED | `scripts/contextual-prefix.py:376` now uses `tmp.write_text() + os.replace(tmp, chunk_path)` matching `bm25-index.py:182` pattern. |
| **H1** `git add` lacks `--` | CLOSED | Bundled with B1; pathspec separator added throughout. |
| **H3** lock-list error has no retry/alert | PARTIAL | Existing `.vault-meta/hook.log` line preserved. Counter + `wiki lint` surface deferred to v1.9.1 (per the audit's own GROW note 5). |
| **H2** cross-process lock release | DEFERRED | Single-tenant design choice; documenting in SECURITY.md is the recommended fix (deferred to v1.9.1). |
| **H4** no stale-lock reaper between sessions | DEFERRED | `wiki-lock.sh clear-stale` exists; wiring it into SessionStart hook + `wiki lint` deferred to v1.9.1. |
| **F1–F5** canonical URL cascade | CLOSED | 8 files updated: `docs/install-guide.md` (version + 4 refs), `CONTRIBUTING.md`, `AGENTS.md`, `GEMINI.md`, `ATTRIBUTION.md`, `.claude-plugin/plugin.json`, `.claude-plugin/marketplace.json`, `docs/releases/v1.6.0.md` (3 image URLs). Plus `wiki/canvases/youtube-explainer.canvas` (2 refs — public-facing YouTube explainer). |
| **W1** 12 dated release notes in wiki/meta/ | **DEFERRED with rationale** | The Files agent's "orphan-ish" claim was disproved on inspection: 9 of the 12 files have incoming wikilinks from `wiki/index.md` + `wiki/entities/Claude SEO.md` + `wiki/folds/`. Moving them would create 6+ NEW dead wikilinks. The Privacy agent's "intentional case-study material" framing is the correct lens. Trim or relocate is tracked for v1.9.2 with explicit wikilink-graph update plan. |
| **W2** 4 wiki files with `agricidaniel` | REASSESSED + PARTIAL | 3 of 4 occurrences are legitimate author self-reference (`agricidaniel.com` blog domain, `@AgriciDaniel` YouTube, `github.com/AgriciDaniel` profile — canonical public identity, not leaks). The 4th file (`wiki/canvases/youtube-explainer.canvas`) contained 2 `AI-Marketing-Hub/claude-obsidian` private-URL refs which were fixed under the canonical-URL cascade (Slice 4). No sanitization needed in `wiki/log.md` or the 2 wiki/meta session notes. |
| **W3** workspace-visual.json tracked | CLOSED | Added to `.gitignore` line 5; `git rm --cached` executed. |
| **S1–S4** security LOW | DEFERRED | Hardening recommendations (Excalidraw checksum, auto-commit gate, lock release docs, ollama-localhost assert). Not blockers; tracked for v1.9.1. |
| **M1–M4 (Data)** | DEFERRED | rerank.py warn-routing, embed-cache GC, symlink canonicalization, locks/.gitkeep. Not blockers; tracked for v1.9.1. |
| **References M1–M2** wiki dead links | DEFERRED | 17 dead wikilink targets across 7 pages; below per-page severity threshold. Tracked with W1 for the same v1.9.2 wiki-cleanup pass. |
| **Files M1–M4** | DEFERRED | Plugin data.json defaults verify, demo-source expansion, wiki/meta size, basename collision check. Tracked for v1.9.2. |
### Re-scored
| Dimension | Pre-fix | Post-fix |
|---|---|---|
| Security | 94 | 94 (no changes; 4 LOW remain) |
| Privacy | 92 | 94 (workspace-visual untracked = +2) |
| Data | 58 | **88** (B1+B2 closed; 4 HIGH remain partially: 1 CLOSED, 1 PARTIAL, 2 DEFERRED) |
| References | 74 | **96** (5 HIGH all closed) |
| Files | 78 | **86** (W3 closed; W1 deferred-with-rationale not deducting; W2 reassessed as non-leak) |
| **OVERALL** | 79 (raw avg) / 70 (BLOCKER-capped) | **91.6** raw avg / **GREEN** (0 BLOCKER) |
### Ship verdict: **GREEN**
Zero BLOCKERs remain. The remaining HIGH findings (H2, H4) are explicitly DEFERRED with rationale (single-tenant design choice documented, stale-lock reaper exists and just needs wiring). Per the audit's own §8 strict gate: GREEN means may proceed to public promotion (still pending user explicit "go").
### Acceptance verification commands (run before commit)
```bash
# B1 + H1 hook safety
python3 -c "import json; json.load(open('hooks/hooks.json'))" # JSON parses
grep -q 'git add -- wiki/' hooks/hooks.json # H1 separator
grep -q 'git commit.*-- wiki/' hooks/hooks.json # B1 commit pathspec
# B2 chunk atomicity
python3 -m py_compile scripts/contextual-prefix.py
grep -q 'os.replace(tmp, chunk_path)' scripts/contextual-prefix.py
# F1-F5 cascade
rg -q 'AgriciDaniel/claude-obsidian' .claude-plugin/plugin.json .claude-plugin/marketplace.json
! rg -q 'raw.githubusercontent.com/AI-Marketing-Hub' docs/releases/v1.6.0.md
# W3 workspace-visual untracked
! git ls-files .obsidian/workspace-visual.json | grep -q .
grep -q 'workspace-visual.json' .gitignore
# Test suite green
make test
```
### Commit plan (4 commits, in execution order)
1. `fix(data): atomic chunk writes via tmp+rename (B2)` — `scripts/contextual-prefix.py`
2. `fix(hooks): pathspec on add+diff+commit prevents auto-commit blast radius (B1+H1+H3)` — `hooks/hooks.json`
3. `fix(docs): cascade canonical URL fix to 9 files (F1-F5)` — install-guide, CONTRIBUTING, AGENTS, GEMINI, ATTRIBUTION, plugin.json, marketplace.json, releases/v1.6.0.md, youtube-explainer.canvas
4. `chore(hygiene): untrack workspace-visual.json + document audit closeout (W3 + audit follow-up)` — .gitignore, workspace-visual.json removal, this audit doc
### Notes current (next slice with rationale)
**v1.9.1** (~2 hours when scheduled): close the 6 DEFERRED HIGH/MEDIUM items from this audit + the audit's own GROW backlog. Specifically: H2 SECURITY.md note on lock semantics, H4 stale-lock reaper wiring, H3 counter + lint surface, Data M1-M4 hardening, Security S1-S4 hardening. None are blockers; they're hygiene polish.
**v1.9.2** (~1 hour when scheduled): wiki/meta/ trim — relocate the 12 dated release-session notes to `docs/releases/` with explicit wikilink-graph update for the 6+ incoming references (`wiki/index.md`, `wiki/entities/Claude SEO.md`, `wiki/folds/fold-k3-...`, `wiki/concepts/Pro Hub Challenge.md`). Plus the 17 wiki dead-link cleanup the References audit M1-M2 surfaced.
Public promotion to `AgriciDaniel/claude-obsidian` remains pending explicit user "go" per standing local-until-explicit-go rule. The post-fix state is shippable; the gate is consent, not quality.
docs/compound-vault-guide.md
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# Compound Vault — v1.7 Guide
**Status:** v1.7.0 (codename "Compound Vault refoundation"), released 2026-05-17
**Audience:** users upgrading from v1.6, new adopters, and skill authors integrating with v1.7+ primitives
**Companion docs:** [dragonscale-guide.md](dragonscale-guide.md) (optional Memory extension), [install-guide.md](install-guide.md), [CHANGELOG.md](../CHANGELOG.md)
---
## Why "Compound Vault"
The v1.7 line introduces a system name — **Compound Vault** — that names the architecture, distinct from the plugin name (`claude-obsidian`). The plugin name stays for SEO continuity and the existing 4.1k+ stars; the system name covers the 13 cohering skills that make the architecture work.
Three-clause positioning:
> *"Compounding vault, not chat. CLI-native, not chat-window. Methodology-aware, not generic."*
- **Compounding vault** — Karpathy's LLM Wiki pattern. Knowledge accumulates across sessions; the wiki gets richer with every ingest.
- **CLI-native** — Obsidian 1.12 made the `obsidian` binary a first-class surface. v1.7 makes it the default transport and demotes MCP to fallback.
- **Methodology-aware** — partial in v1.7 (modes ship in v1.8). The framing already shapes the v1.7 scope.
Drop-in tagline candidate (for blog/marketing):
> **"Karpathy's wiki, in your Obsidian."**
---
## What changed from v1.6 (executive summary)
v1.7 ships in four workstreams (§3.1 substrate / §3.2 transport / §3.3 retrieval / §3.4 concurrency), each one independent enough to roll back if it causes trouble. None are breaking — a v1.6 vault that does nothing on upgrade continues to behave exactly as v1.6.
| Workstream | What | Why | Adopter action |
|---|---|---|---|
| §3.1 Substrate | 3 skills upgrade soft-defer → hard-prefer for `kepano/obsidian-skills` | Stop competing with the platform owner | `claude plugin marketplace add kepano/obsidian-skills` (recommended) |
| §3.2 Transport | New `wiki-cli` skill + `detect-transport.sh` + decision tree | Obsidian 1.12 CLI is the fastest, safest write path | None — auto-detected on first session |
| §3.3 Retrieval | New `wiki-retrieve` skill + contextual prefix + BM25 + cosine rerank | Anthropic Sept 2024 research: 35-67% retrieval-failure reduction | `bash bin/setup-retrieve.sh` (opt-in) |
| §3.4 Concurrency | New `wiki-lock.sh` + 4 skill guards + hook debounce | Close the latent multi-writer corruption bug | None — universally beneficial, no setup |
---
## §3.1 Substrate dependency on kepano/obsidian-skills
**What it is:** Three claude-obsidian skills (`obsidian-markdown`, `obsidian-bases`, `canvas`) overlap with skills in `kepano/obsidian-skills` (by Steph Ango, Obsidian's CEO). In v1.6 we soft-deferred ("if kepano is installed, prefer it"). In v1.7 we hard-prefer: kepano is canonical; our copies are the floor.
**Why:** Continuing to ship parallel implementations of platform-owner primitives is a structural losing fight. The kepano marketplace has 30.5k+ stars; we have 4.1k+. Adopting kepano as substrate signals alignment and frees us to invest in the *workflow* layer (ingest, query, lint, autoresearch, save, retrieve) that no one else owns.
**What changed in the codebase:**
- `skills/obsidian-markdown/SKILL.md:11` — preface rewrites to "This skill is a self-contained fallback. Prefer `kepano/obsidian-skills`."
- `skills/obsidian-bases/SKILL.md:11` — same pattern.
- `skills/canvas/SKILL.md:14` — same pattern (json-canvas spec defers to kepano; wiki-scoped workflows stay claude-obsidian's).
- `skills/defuddle/SKILL.md:11` — documented as canonical (kepano does not ship a defuddle skill).
- `.claude-plugin/marketplace.json` — `recommendedCompanions` array names `kepano/obsidian-skills` with install hint, rationale, and repo link.
**Adopter action:** Run `claude plugin marketplace add kepano/obsidian-skills`. Existing skills keep working without it (the local fallbacks remain functional).
---
## §3.2 Default transport — Obsidian CLI with fallback chain
**What it is:** A four-tier transport stack with auto-detection. New skill `wiki-cli` documents the CLI recipes. New script `scripts/detect-transport.sh` writes `.vault-meta/transport.json` so other skills can consult it.
Fallback chain (highest to lowest precedence):
1. **cli** — `obsidian-cli` binary (Obsidian 1.12+). No MCP server, no TLS, no plugin.
2. **mcp-obsidian** — REST-API-backed MCP server (Local REST API plugin required). Auto-detection deferred to v1.7.x.
3. **mcpvault** — Filesystem-backed MCP server (BM25 search; no Obsidian plugin). Auto-detection deferred.
4. **filesystem** — Direct `Read`/`Write`/`Edit` tools. Always available; the floor.
**Why:** v1.6 documented four equal transports. Skills used direct `Read`/`Write` by default. v1.7 sharpens the recommendation and makes selection a one-line lookup against `.vault-meta/transport.json`.
**Architecture:**
```
detect-transport.sh (run at session start or vault setup)
│
└─ writes → .vault-meta/transport.json
{
"preferred": "cli" | "filesystem",
"fallback_chain": [...],
"available": { cli: {...}, filesystem: {...}, mcp_obsidian: null, mcpvault: null }
}
skills (wiki-ingest, wiki-query, save, autoresearch, wiki-lint):
├─ each has a "## Transport (v1.7+)" section near the top
├─ reads transport.json at runtime
└─ uses obsidian-cli if "preferred": "cli", else Read/Write
```
**Adopter action:** None — the detection runs automatically and refreshes after 7 days. To force a refresh: `bash scripts/detect-transport.sh --force`. To manually pin to an MCP transport, edit `.vault-meta/transport.json` and set `"manual_override": true` so the detection script leaves your edit alone.
**See:** [`wiki/references/transport-fallback.md`](../wiki/references/transport-fallback.md) for the full decision tree and [`skills/wiki-cli/SKILL.md`](../skills/wiki-cli/SKILL.md) for the per-operation recipes.
---
## §3.3 Hybrid retrieval pipeline — wiki-retrieve (opt-in)
**What it is:** A new opt-in skill that replaces the v1.6 static `Read(hot.md) → Read(index.md) → Read(N pages)` query path with chunk-level retrieval using BM25 + cosine rerank over contextually-prefixed chunks. Implements Anthropic's [Sept 2024 Contextual Retrieval](https://www.anthropic.com/news/contextual-retrieval) pattern as agent-skill plumbing.
**Why:** Page-level granularity loses to chunk-level granularity any time the answer lives in a specific passage. Anthropic measured a 35% retrieval-failure reduction from contextual prefixes, 49% from hybrid BM25+vector, and 67% from adding a reranker. v1.7 implements the contextual + sparse + rerank stack. (A separate dense vector stage is on the v1.7.x roadmap.)
**Architecture:**
```
INGEST (one-time + incremental):
wiki/<page>.md
│
▼
scripts/contextual-prefix.py
│ ├─ chunks on paragraph boundaries (~500 tokens target, 200 char overlap)
│ └─ generates 1-2 sentence prefix per chunk
│ tier 1: ANTHROPIC_API_KEY → Anthropic API (Haiku, prompt-cached
│ when body ≥ ~16 KB / Haiku 4.5 floor)
│ tier 2: claude on PATH → `claude -p` subprocess
│ tier 3: synthetic → frontmatter title + first paragraph
│
▼ .vault-meta/chunks/<address>/chunk-NNN.json
scripts/bm25-index.py build
└─ inverted index over chunks' contextualized_text → .vault-meta/bm25/index.json
QUERY:
query string
│
▼
scripts/retrieve.py "<query>" --top 5
├─ scripts/bm25-index.py query → top-20 candidates by BM25
├─ scripts/rerank.py → cosine on nomic-embed-text via ollama
│ (no-op if ollama unreachable; BM25 order preserved)
└─ page-address dedupe → final top-5 with absolute_path
│
▼
caller (wiki-query / autoresearch) reads cited pages and synthesizes
```
**Feature gating:** Other skills detect wiki-retrieve via:
```bash
[ -x scripts/retrieve.py ] && [ -d .vault-meta/chunks ] && [ -f .vault-meta/bm25/index.json ]
```
If detection fails, skills fall back to the v1.6 legacy read order. The skill never breaks the base plugin.
**Cost ceiling:** ~$12 per 1,000 documents per Anthropic's published figure (Haiku + prompt caching, tier 1). Tier 2 (claude CLI) is free in dollars but slower. Tier 3 (synthetic) is free and hermetic; loses most of the contextual benefit but BM25 + rerank still work.
**Adopter action:**
```bash
bash bin/setup-retrieve.sh # full provisioning (auto-picks prefix tier)
bash bin/setup-retrieve.sh --no-llm # force tier 3 (zero LLM dependency)
bash bin/setup-retrieve.sh --check # diagnostics only; no provisioning
```
After setup, `wiki-query` standard/deep modes automatically use the new pipeline. Quick mode (hot.md only) is unchanged.
**See:** [`skills/wiki-retrieve/SKILL.md`](../skills/wiki-retrieve/SKILL.md) for the full skill spec, recipe reference, and v1.7.x roadmap (BGE cross-encoder, Cohere Rerank, separate dense vector stage).
---
## §3.4 Multi-writer safety — wiki-lock (core)
**What it is:** Per-file advisory locking via `scripts/wiki-lock.sh`. Every wiki page write MUST be preceded by `wiki-lock acquire <path>` and followed by `wiki-lock release <path>`.
**Why:** v1.6 had a latent corruption bug. `skills/wiki-ingest/SKILL.md:259-264` documented "single-writer only" as a convention, but the actual page-write paths had no enforcement. Two parallel sub-agents writing to the same wiki page could silently trample each other. The Karpathy-LLM-Wiki-Stack README explicitly warned about this. v1.7 closes the hole.
**Design (age-based, not flock-style):**
`flock(2)` advisory locks release when the holding process exits. That doesn't fit our model where `acquire` and `release` are SEPARATE bash invocations from the same skill (each Bash tool call is its own short-lived process — neither's PID survives long enough to mean anything). So `wiki-lock.sh` uses:
- **Atomic noclobber-write of a lockfile** (race-safe on POSIX filesystems).
- **Epoch-based AGE staleness**: a lock older than `STALE_AFTER_SEC` (default 60) is auto-reaped. Crashed holders unblock in ≤60s without manual intervention.
- **Cross-process release allowed**: `release` is `rm -f` (no PID match required). Skill authors are trusted to release locks they acquire. The `wiki-lock clear-stale --max-age 0` command is the canonical recovery path.
- **PID in the lockfile is informational only** (helpful for `list` and debugging).
**Skill integration:**
Four skills gained "## Concurrency (v1.7+)" sections with the recipe:
```bash
if bash scripts/wiki-lock.sh acquire wiki/concepts/Foo.md; then
# … do the write via the §Transport-selected method …
bash scripts/wiki-lock.sh release wiki/concepts/Foo.md
else
# rc=75 = EX_TEMPFAIL = another writer in flight. Retry once after 2s;
# if still held, log to wiki/log.md and skip this page.
sleep 2
bash scripts/wiki-lock.sh acquire wiki/concepts/Foo.md && {
# write …
bash scripts/wiki-lock.sh release wiki/concepts/Foo.md
} || echo "skipped wiki/concepts/Foo.md (locked)"
fi
```
**Hook integration:** `hooks/hooks.json` PostToolUse now defers `git add` if any locks are currently held. Prevents torn commits during multi-agent ingest. Falls through gracefully when `wiki-lock.sh` is absent.
**Adopter action:** None — `wiki-lock.sh` is core in v1.7 (no opt-in). Sub-agents that don't follow the acquire/release pattern are racing against any other writer (as before — but now there's a tool to fix it).
**Test coverage:** `tests/test_wiki_lock.sh` (14 hermetic assertions) and `tests/test_concurrent_write.sh` (the critical correctness gate — 10 parallel workers, no losses, no garbled lines). `make test-concurrent` and `make test-lock`.
**See:** [`scripts/wiki-lock.sh`](../scripts/wiki-lock.sh) header comments for the full semantics, and `skills/wiki-ingest/SKILL.md` §Concurrency for the canonical integration pattern.
---
## Skill inventory (v1.7)
13 skills total. New in v1.7: `wiki-cli`, `wiki-retrieve`.
| Skill | Status | Role |
|---|---|---|
| `wiki` | core | Setup / scaffold / sub-skill router |
| `wiki-ingest` | core | Source → wiki pages with cross-refs |
| `wiki-query` | core | Question answering (now uses wiki-retrieve if installed) |
| `wiki-lint` | core | Health check (orphans, dead links, addresses, tiling) |
| `wiki-fold` | DragonScale Mech 1 | Extractive log rollups |
| `wiki-cli` | **new in v1.7 (§3.2)** | Obsidian CLI transport wrapper |
| `wiki-retrieve` | **new in v1.7 (§3.3, opt-in)** | Contextual + BM25 + rerank |
| `save` | core | File conversations as wiki notes |
| `autoresearch` | core | Iterative web research → wiki |
| `canvas` | core (defers to kepano json-canvas) | Visual wiki layer |
| `defuddle` | core (canonical) | Web page cleaner |
| `obsidian-markdown` | core (defers to kepano) | Obsidian Flavored Markdown reference |
| `obsidian-bases` | core (defers to kepano) | Bases YAML reference |
---
## Scripts inventory (v1.7)
| Script | Status | Role |
|---|---|---|
| `allocate-address.sh` | DragonScale Mech 2 | Atomic c-NNNNNN allocator (flock) |
| `tiling-check.py` | DragonScale Mech 3 | Embedding-based duplicate lint (fcntl) |
| `boundary-score.py` | DragonScale Mech 4 | Frontier scoring for autoresearch |
| `detect-transport.sh` | **new in v1.7 (§3.2)** | Transport detection → transport.json |
| `contextual-prefix.py` | **new in v1.7 (§3.3)** | Chunk + 3-tier prefix generation |
| `bm25-index.py` | **new in v1.7 (§3.3)** | Sparse inverted index (flock) |
| `rerank.py` | **new in v1.7 (§3.3)** | Cosine rerank via ollama (fcntl on cache) |
| `retrieve.py` | **new in v1.7 (§3.3)** | Hybrid retrieval orchestrator |
| `wiki-lock.sh` | **new in v1.7 (§3.4)** | Per-file advisory locks (noclobber) |
---
## Tests (v1.7)
`make test` runs 7 suites. All hermetic — zero network, zero ollama, zero LLM calls.
| Target | File | Assertions | Coverage |
|---|---|---|---|
| `make test-address` | `tests/test_allocate_address.sh` | ~10 | DragonScale Mech 2 |
| `make test-tiling` | `tests/test_tiling_check.py` | ~15 | DragonScale Mech 3 |
| `make test-boundary` | `tests/test_boundary_score.py` | ~35 | DragonScale Mech 4 |
| `make test-bm25` | `tests/test_bm25_index.py` | ~30 | tokenize, BM25 monotonicity, IDF |
| `make test-retrieve` | `tests/test_retrieve.py` | 22 | cosine, rerank, end-to-end subprocess |
| `make test-lock` | `tests/test_wiki_lock.sh` | 14 | acquire, release, age-based reap |
| `make test-concurrent` | `tests/test_concurrent_write.sh` | 6 | **the critical multi-writer correctness gate** |
The "hermetic test invariant" is preserved: nothing in `make test` requires the network, ollama, or any API key. Optional pipelines (contextual prefix with Anthropic API, rerank with ollama cosine) are tested via mocks and graceful fallbacks.
---
## What v1.7 is NOT
- Not a rewrite. DragonScale Mechanisms 1-4 are preserved and unchanged.
- Not a breaking change. v1.6 vaults that don't run setup-retrieve.sh see no behavior difference (modulo the wiki-lock integration, which is universally beneficial and adds no setup).
- Not a paid plugin. License stays MIT.
- Not a GUI Obsidian-plugin shell. Deferred to v2.5+ (the Claudian/deivid11 wrapper pattern is item #7 in the May 2026 gap-analysis backlog).
- Not multi-vault federation. Deferred to v2.x.
---
## Roadmap pointers
The May 2026 gap analysis identified 20 backlog items. v1.7 ships items 1, 2, 3, 4 (the top-quartile by value/effort) plus the latent-bug fix. Next milestones (subject to user prioritization):
- **v1.8** — Methodology modes (LYT / PARA / Zettelkasten / Generic via `wiki-mode`) + periodic reviews (`wiki-review`). Closes gaps #6 + #11.
- **v1.9** — Multimodal ingest adapters (YouTube, PDF, EPUB, image OCR via `wiki-ingest-multimodal`). Closes gaps #8 + #12.
- **v2.0** — NotebookLM-class derivative outputs (audio, quiz, flashcards, study guide via `wiki-derive`). Closes gaps #5 + #9 + #14.
Full plan: `~/.claude/plans/read-in-full-the-hidden-sun.md`.
---
## See also
- [CHANGELOG.md](../CHANGELOG.md) — v1.7.0 entry
- [docs/dragonscale-guide.md](dragonscale-guide.md) — DragonScale Memory extension (Mechanisms 1-4)
- [docs/install-guide.md](install-guide.md) — installation
- [wiki/references/transport-fallback.md](../wiki/references/transport-fallback.md) — transport decision tree
- [wiki/concepts/DragonScale Memory.md](../wiki/concepts/DragonScale%20Memory.md) — spec
- Anthropic Contextual Retrieval: https://www.anthropic.com/news/contextual-retrieval
- kepano/obsidian-skills: https://github.com/kepano/obsidian-skills
- Karpathy LLM Wiki gist: https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f
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# DragonScale Memory Guide
DragonScale Memory is an optional extension for `claude-obsidian`. It adds conservative helpers for log rollups, stable page addresses, duplicate-page linting, and frontier topic suggestion. Start with [docs/install-guide.md](./install-guide.md). For the design spec and rationale, read [wiki/concepts/DragonScale Memory.md](../wiki/concepts/DragonScale%20Memory.md).
This page stays close to shipped behavior in `v1.6.0`. It explains what setup creates, what each mechanism actually does, what it needs, and how to turn it off safely without uninstalling the repo.
## What DragonScale Is
### Scope and opt-in status
DragonScale is a memory-layer extension for the wiki. It covers rollups, deterministic page IDs, duplicate detection, and one opt-in topic-selection path for `/autoresearch`. It is not required for the base vault.
If you never run `bash bin/setup-dragonscale.sh`, the base install and the original skill behavior remain in place. The repo uses feature detection so DragonScale can stay optional instead of becoming a hard dependency.
The concept page is broader than this guide. This guide is operational. When the spec and implementation differ in detail, prefer the shipped scripts and skills for day-to-day behavior.
### What ships in 1.6.0
Version `1.6.0` ships all four DragonScale mechanisms as opt-in features:
- Mechanism 1, Fold Operator: `skills/wiki-fold/`
- Mechanism 2, Deterministic Page Addresses: `scripts/allocate-address.sh` plus `wiki-ingest` and `wiki-lint` integration
- Mechanism 3, Semantic Tiling Lint: `scripts/tiling-check.py` plus `wiki-lint` integration
- Mechanism 4, Boundary-First Autoresearch: `scripts/boundary-score.py` plus `skills/autoresearch/SKILL.md` Topic Selection logic
Use `CHANGELOG.md` for the release trail, [docs/install-guide.md](./install-guide.md) for the quick-start view, and [wiki/concepts/DragonScale Memory.md](../wiki/concepts/DragonScale%20Memory.md) for the full design context.
## Before You Enable It
### Base install requirements
DragonScale is an add-on, not a replacement for base setup. Do the normal vault install first by following [docs/install-guide.md](./install-guide.md).
At minimum:
- clone the repo or install the plugin
- run `bash bin/setup-vault.sh`
- open the folder as an Obsidian vault
- use `/wiki` to scaffold or continue setup
The DragonScale setup script accepts one optional argument, the vault path:
```bash
bash bin/setup-dragonscale.sh
```
```bash
bash bin/setup-dragonscale.sh /path/to/vault
```
If you omit the path, it uses the repo root inferred from `bin/`.
### Universal prerequisite: flock
`flock` is the universal prerequisite. Mechanism 2 uses it directly in `scripts/allocate-address.sh` to guard `.vault-meta/.address.lock`. Mechanism 3 uses flock from Python to guard `.vault-meta/.tiling.lock` around cache I/O.
Quick check:
```bash
command -v flock
```
If that prints nothing, install `flock` before relying on DragonScale. On Linux it is usually already present. On macOS it commonly comes from `util-linux`.
If `flock` is missing, setup can still create files, but the address allocator and tiling cache path are not reliable. Treat that as a blocker.
### Mechanism 3 extra prerequisites: python3, ollama, nomic-embed-text
Mechanism 3 is the only mechanism with the full local embeddings stack. You need `python3`, `ollama`, and the `nomic-embed-text` model pulled into ollama.
Useful checks:
```bash
command -v python3
```
```bash
curl -sS http://127.0.0.1:11434/api/version
```
```bash
ollama pull nomic-embed-text
```
The setup script does not install any of those. It only checks and reports status. Mechanism 4 needs `python3`, but not ollama. Mechanisms 1 and 2 do not need either.
### What happens when optional deps are missing
DragonScale is meant to fail closed or no-op cleanly.
If `python3` is missing:
- Mechanism 3 cannot run
- Mechanism 4 cannot run
- Mechanisms 1 and 2 still work
If ollama is unreachable, `scripts/tiling-check.py` exits `10`. If ollama is reachable but `nomic-embed-text` is not installed, it exits `11`. `wiki-lint` is expected to treat those as skip conditions for semantic tiling, not as a reason to break the rest of the lint flow.
If the boundary helper fails, `/autoresearch` falls back to the normal ask-the-user topic path. It does not force a candidate list and it does not improvise a topic.
If DragonScale setup has never been run, `wiki-ingest` and `wiki-lint` keep their non-DragonScale behavior.
## Setup
### Run bin/setup-dragonscale.sh
Run:
```bash
bash bin/setup-dragonscale.sh
```
The script is idempotent. It is safe to re-run and it does not overwrite the runtime files it already created.
Before provisioning state, it verifies:
- `scripts/allocate-address.sh`
- `scripts/tiling-check.py`
- `skills/wiki-fold/SKILL.md`
If any of those are missing, setup stops and tells you to reinstall the plugin.
What setup does:
- makes `scripts/allocate-address.sh` executable
- makes `scripts/tiling-check.py` executable
- creates `.vault-meta/` if needed
- creates address, tiling, and legacy-baseline state files if missing
- creates `.raw/.manifest.json` if missing
- runs sanity checks at the end
What setup does not do:
- install ollama
- pull `nomic-embed-text`
- backfill addresses onto old pages
- run a fold
- run semantic tiling
- rewrite your existing wiki pages
### What files and state it creates
Setup provisions a small amount of runtime state.
In `.vault-meta/` it creates:
- `address-counter.txt`
- `tiling-thresholds.json`
- `legacy-pages.txt`
In `.raw/` it creates:
- `.manifest.json`
`address-counter.txt` starts at `1`, so the next reserved page address in a brand-new vault will be `c-000001`.
`tiling-thresholds.json` is seeded with `error: 0.90`, `review: 0.80`, and `calibrated: false`. These are conservative seed bands, not calibrated truth for your vault.
`legacy-pages.txt` gets a rollout marker comment:
```text
# rollout: YYYY-MM-DD
```
`wiki-lint` uses that baseline to separate legacy pages from post-rollout pages for address enforcement.
`.raw/.manifest.json` starts with empty `sources` and `address_map` objects. The ingest skill maintains that file. The source documents under `.raw/` remain immutable.
### How to verify setup
The setup script already performs sanity checks, but it is useful to verify a few things yourself.
Check the next address without reserving one:
```bash
./scripts/allocate-address.sh --peek
```
Check that runtime state exists:
```bash
ls -1 .vault-meta
```
Check tiling readiness without computing embeddings:
```bash
python3 ./scripts/tiling-check.py --peek
```
Check the boundary helper:
```bash
python3 ./scripts/boundary-score.py --top 5
```
If your vault is small or tightly integrated, the boundary helper may report no positive-score frontier pages. That is still a valid run.
## Mechanism 1: Fold Operator
### What it does
The fold operator is a log rollup. It reads the most recent `2^k` entries from `wiki/log.md` and produces an extractive fold page under `wiki/folds/`.
The fold is additive. It does not delete, move, or rewrite the child entries. The fold is extractive. Every outcome and theme in the output must be traceable to a child log entry.
The current shipped skill is intentionally narrow. It supports a flat fold over raw log entries. Hierarchical fold-of-folds behavior remains outside the scope of the current skill even though the concept spec discusses stacked folds.
The fold ID is deterministic for a given range:
```text
fold-k{K}-from-{EARLIEST-DATE}-to-{LATEST-DATE}-n{COUNT}
```
That gives structural idempotency. If the exact fold already exists, the skill should stop instead of writing a duplicate.
### When to use it
Use a fold when the log has accumulated a coherent batch of work and you want a checkpoint page that is easier to scan than a raw run of entries.
Typical cases:
- after several ingests on one theme
- after a burst of research sessions
- before a long flat `wiki/log.md` gets harder to use
Do not treat folds as garbage collection. They summarize. They do not compact by deletion.
Example command:
```text
fold the log, dry-run k=3
```
That asks for a dry-run over `2^3 = 8` entries.
### Dry-run vs commit mode
Dry-run is the default and it is stdout-only. That matters because the repo has a PostToolUse hook for writes.
In dry-run mode:
- no file is written
- no auto-commit hook is triggered
- you get the proposed fold content in the terminal output
In commit mode:
- the fold page is written to `wiki/folds/`
- `wiki/index.md` is updated
- `wiki/log.md` gets a new fold entry
The skill docs expect three separate write operations in commit mode, so three auto-commits from the hook are normal.
Example commit command:
```text
fold the log, commit k=3
```
Run a dry-run first. Commit only if the fold content looks right.
To disable Mechanism 1 without uninstalling DragonScale, stop invoking `wiki-fold`. Existing fold pages can remain in the vault, or you can remove them manually if you no longer want them.
## Mechanism 2: Deterministic Page Addresses
### Address format and rollout policy
Mechanism 2 assigns stable frontmatter addresses. The shipped format is:
```yaml
address: c-000042
```
`c-` means creation-order counter. The numeric part is zero-padded to six digits. This is not a content hash. The spec is explicit that the shipped address is deterministic and stable, but not content-addressable.
The rollout baseline is `2026-04-23`. After DragonScale adoption, post-rollout non-meta pages are expected to have addresses. Legacy pages are exempt until you do a deliberate backfill.
The helper has three real modes:
```bash
./scripts/allocate-address.sh
```
```bash
./scripts/allocate-address.sh --peek
```
```bash
./scripts/allocate-address.sh --rebuild
```
The default mode reserves and prints the next address. `--peek` is read-only. `--rebuild` recomputes the counter from the highest observed `c-NNNNNN`.
Example command:
```bash
./scripts/allocate-address.sh --peek
```
### How ingest and lint use it
`wiki-ingest` enables address assignment only when `./scripts/allocate-address.sh` is executable and `./.vault-meta` exists. If both conditions are true, new non-meta pages get `address:` in frontmatter. If not, ingest proceeds without addresses.
`wiki-lint` enables address validation only when `./scripts/allocate-address.sh` is executable and `./.vault-meta/address-counter.txt` exists. If those conditions are true, lint checks address format, uniqueness, counter consistency against `--peek`, missing addresses on post-rollout pages, and `address_map` consistency in `.raw/.manifest.json`.
The single-writer rule matters here. The allocator uses `flock`, but the ingest skill still says Phase 2 is single-writer only. Do not run parallel ingests from multiple sessions or sub-agents that assign addresses.
One hard rule from the skill docs is worth repeating. Never edit `.vault-meta/address-counter.txt` directly. Only mutate it through `scripts/allocate-address.sh`.
To disable Mechanism 2 without uninstalling:
1. stop running ingests that depend on address assignment
2. remove `.vault-meta/` if you want feature detection to turn off
3. stop using `./scripts/allocate-address.sh`
Existing `address:` fields can stay on pages. They become inert metadata if the feature is disabled.
## Mechanism 3: Semantic Tiling Lint
### What it checks
Mechanism 3 is an embedding-based duplicate-page detector. It scans markdown files under `wiki/` and excludes:
- `wiki/folds/`
- `wiki/meta/`
- common meta filenames such as `index.md`, `log.md`, `hot.md`, `overview.md`, `dashboard.md`, `Wiki Map.md`, and `getting-started.md`
- files with `type: meta`
- files with `type: fold`
- symlinks or paths that escape the vault root
It computes one embedding per included page, compares pairs by cosine similarity, and emits candidate overlap in bands.
Default bands:
- `>= 0.90` as error
- `0.80 - 0.90` as review
- `< 0.80` as pass
The helper never auto-merges pages. It only reports candidates for review.
Example command:
```bash
python3 ./scripts/tiling-check.py --peek
```
That gives structured diagnostics without computing embeddings.
### Local embeddings requirement
By default, the helper only trusts a local ollama endpoint at `http://127.0.0.1:11434`. Remote ollama endpoints require an explicit override flag because page bodies are sent as embedding input.
Remote override example:
```bash
python3 ./scripts/tiling-check.py --allow-remote-ollama --peek
```
The normal ready path is local:
1. `python3` is installed
2. ollama is reachable on localhost
3. `nomic-embed-text` is installed in ollama
Important exit codes:
- `0` success
- `10` ollama unreachable
- `11` model missing
`wiki-lint` is written to treat those as skip conditions.
### Calibration and no-op behavior
The shipped thresholds are conservative seeds, not calibrated truth. The skill docs call for a manual one-time calibration pass per vault. Until you do that, expect both false negatives and false positives.
The helper also has intentional no-op behavior. If ollama or the model is missing, it exits with the skip code. It does not fake results.
Useful commands:
```bash
python3 ./scripts/tiling-check.py --peek
```
```bash
python3 ./scripts/tiling-check.py --rebuild-cache
```
```bash
python3 ./scripts/tiling-check.py --report wiki/meta/tiling-report-YYYY-MM-DD.md
```
`--report` is real and path-confined to the vault. Use it when you want a saved report. Use `--peek` when you only want readiness and diagnostics.
To disable Mechanism 3 without uninstalling:
1. stop running `python3 ./scripts/tiling-check.py`
2. stop using the semantic-tiling path in `wiki-lint`
3. do not provision ollama or the model if you do not need them
Note that `.vault-meta/` is a shared gate for Mechanisms 2, 3, and 4. Do not remove it to disable Mechanism 3 alone, or you will also turn off address allocation and boundary-first autoresearch. The tiling cache lives under `.vault-meta/` but is inert when the helper is not invoked.
## Mechanism 4: Boundary-First Autoresearch
### What it does
Mechanism 4 scores frontier pages in the wiki graph. The shipped formula is:
```text
boundary_score(p) = (out_degree(p) - in_degree(p)) * recency_weight(p)
```
In practice, high-score pages point outward to many scoreable pages, receive relatively fewer inbound links, and were updated recently enough to still be frontier-like.
The helper reads `wiki/**/*.md`, builds a wikilink graph, and emits ranked results to stdout or JSON. It is intentionally stdout-only. Unlike the tiling helper, it has no `--report PATH` mode.
Example command:
```bash
python3 ./scripts/boundary-score.py --json --top 5
```
That is the exact command the autoresearch skill uses for candidate generation.
### Agenda-control caveat
This caveat is explicit in both the spec and the skill docs.
This is agenda control, not pure memory.
Mechanism 4 does not just describe the vault. It influences what the agent is likely to research next. That crosses the memory and planning boundary.
The project keeps it opt-in and labels it honestly. If you want the strict memory-layer subset only, omit this path. Do not use `/autoresearch` without a topic, or do not set up and invoke the boundary scorer.
### How /autoresearch behaves with and without it
With Mechanism 4 available, and only when `/autoresearch` is invoked without a topic, the skill:
1. checks for `scripts/boundary-score.py`
2. checks for `./.vault-meta`
3. checks for `python3`
4. runs `./scripts/boundary-score.py --json --top 5`
5. presents the top frontier pages as candidate topics
6. lets the user pick, override with free text, or decline
If the helper exits non-zero, returns invalid JSON, or returns an empty `results` array, the skill falls back.
Without Mechanism 4, or after fallback, `/autoresearch` simply asks:
```text
What topic should I research?
```
The helper suggests. The user still decides.
To disable Mechanism 4 without uninstalling:
1. stop running `python3 ./scripts/boundary-score.py`
2. use `/autoresearch [topic]` with an explicit topic
3. avoid the no-topic `/autoresearch` path if you do not want frontier suggestions
Note that `.vault-meta/` is a shared gate for Mechanisms 2, 3, and 4. Do not remove it to disable Mechanism 4 alone. The scorer itself is read-only and uses no shared state; disabling it just means not invoking it.
## Operational Policies
### Single-writer rule
DragonScale assumes a single writer for the address-assignment path. The allocator is flock-guarded, which protects the counter from simple races. It does not turn the whole wiki into a safe multi-writer system.
The ingest skill is explicit here. Do not run parallel ingests from multiple Claude sessions or sub-agents that assign addresses.
The safe operating policy is:
- one active ingest writer at a time
- one address allocator path at a time
- no direct manual edits to counter state
Mechanism 1 is human-invoked and easy to serialize. Mechanism 3 uses a lock for cache I/O. Mechanism 4 is read-only.
### Feature detection and graceful fallback
DragonScale is meant to be feature-detected, not assumed.
`wiki-ingest` only assigns addresses when the allocator is executable and `.vault-meta/` exists.
`wiki-lint` only validates addresses when the allocator exists and `.vault-meta/address-counter.txt` exists.
`wiki-lint` only runs semantic tiling when the helper exists and `python3` is available, then interprets readiness from `--peek`.
`autoresearch` only uses boundary-first selection when the helper exists, `.vault-meta/` exists, and `python3` is present.
When those conditions are not met, the repo falls back to earlier behavior. That is the intended operational posture.
## Troubleshooting
### Missing flock
If `flock` is missing, fix that first. Symptoms can include an unsafe address-allocation path or a tiling cache path that cannot lock correctly.
Check:
```bash
command -v flock
```
If it is absent, install the package that provides it for your system, then rerun:
```bash
bash bin/setup-dragonscale.sh
```
Do not work around this by editing `.vault-meta/address-counter.txt` directly.
### Missing ollama or model
This only blocks Mechanism 3. It does not block the rest of DragonScale.
Check ollama reachability:
```bash
curl -sS http://127.0.0.1:11434/api/version
```
Check tiling readiness:
```bash
python3 ./scripts/tiling-check.py --peek
```
If the helper exits `10`, ollama is not reachable. If it exits `11`, pull the model:
```bash
ollama pull nomic-embed-text
```
Then rerun:
```bash
python3 ./scripts/tiling-check.py --peek
```
Remember that Mechanism 4 does not need ollama. If you only want boundary-first autoresearch, `python3` is enough.
### Safe rollback / disable path
You do not need to uninstall the repo to turn DragonScale off. Use the smallest rollback that fits what you want:
- Mechanism 1: stop invoking `wiki-fold`. It uses no shared state.
- Mechanism 2: stop using `./scripts/allocate-address.sh`. Existing `address:` frontmatter fields remain as plain content.
- Mechanism 3: stop running `python3 ./scripts/tiling-check.py` and stop invoking the semantic-tiling path in `wiki-lint`. Cache under `.vault-meta/` is inert when not used.
- Mechanism 4: stop running `python3 ./scripts/boundary-score.py` and avoid the no-topic `/autoresearch` path. The scorer is read-only; disabling is not invoking it.
`.vault-meta/` is a shared gate for Mechanisms 2, 3, and 4. Removing it disables all three together, not just one.
If you want to disable DragonScale feature detection across the setup-based mechanisms at once, remove `.vault-meta/`:
```bash
rm -rf .vault-meta
```
Then stop invoking the DragonScale-specific helpers and skills. This leaves your normal wiki content intact. It does not remove fold pages, and it does not strip existing `address:` fields from frontmatter. Those remain as plain content unless you choose to clean them up manually.
If you later want DragonScale back, rerun:
```bash
bash bin/setup-dragonscale.sh
```
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# claude-obsidian: Install Guide
**Claude + Obsidian Knowledge Companion**
Version 1.9.2 · public canonical: [github.com/AgriciDaniel/claude-obsidian](https://github.com/AgriciDaniel/claude-obsidian) · community early-access mirror (Pro): [AI Marketing Hub org](https://github.com/AI-Marketing-Hub)
> ℹ️ The install commands below use the **public open-source** URLs (`AgriciDaniel/claude-obsidian`), recommended for everyone and requiring no membership. [AI Marketing Hub Pro](https://www.skool.com/ai-marketing-hub-pro) members who want early access to in-development features can swap every `AgriciDaniel/claude-obsidian` for `AI-Marketing-Hub/claude-obsidian` and the plugin slug `claude-obsidian@agricidaniel-claude-obsidian` for `claude-obsidian@ai-marketing-hub-claude-obsidian`.
> **Optional: DragonScale Memory extension.** If you want flat extractive log folds, deterministic page addresses, semantic tiling lint, and boundary-first autoresearch topic selection, run `bash bin/setup-dragonscale.sh` after the base install. Extra prerequisites beyond the base: `flock` (standard on Linux; available via `util-linux` on macOS) and `python3` (for the tiling and boundary helpers). Optional: `ollama` with `nomic-embed-text` pulled if you want the semantic tiling lint (Mechanism 3 only; it no-ops gracefully when ollama or the model is unavailable). The boundary-first scorer (Mechanism 4) needs only `python3`, no ollama. See [`docs/dragonscale-guide.md`](./dragonscale-guide.md) for the user-facing guide, `wiki/concepts/DragonScale Memory.md` for the full spec, and `CHANGELOG.md` for what shipped in 1.6.0.
---
## What is claude-obsidian?
claude-obsidian is a Claude Code plugin + Obsidian vault that builds and maintains a persistent, compounding knowledge base. Every source you add gets processed into cross-referenced wiki pages. Every question you ask pulls from everything that has been read. Knowledge compounds like interest.
Built on Andrej Karpathy's LLM Wiki pattern.
---
## Prerequisites
| Tool | How to get it | Notes |
|------|--------------|-------|
| **Claude Code** | `npm install -g @anthropic-ai/claude-code` | Free tier available |
| **Obsidian** | [obsidian.md](https://obsidian.md) | Free |
| **Git** | Pre-installed on most systems | For Option 1 |
---
## Installation
### Option 1: Clone as vault (recommended)
Full setup in under 2 minutes.
```bash
git clone https://github.com/AgriciDaniel/claude-obsidian
cd claude-obsidian
bash bin/setup-vault.sh
```
Then in Obsidian: **Manage Vaults → Open folder as vault → select `claude-obsidian/`**
Open Claude Code in the same folder and type `/wiki`.
### Option 2: Install as Claude Code plugin
Plugin installation in Claude Code is a two-step process. First add the marketplace catalog, then install the plugin from it.
```bash
# Step 1: add the marketplace
claude plugin marketplace add AgriciDaniel/claude-obsidian
# Step 2: install the plugin
claude plugin install claude-obsidian@agricidaniel-claude-obsidian
```
Verify the install:
```bash
claude plugin list
```
In any Claude Code session: type `/wiki` and Claude walks you through vault setup.
### Option 3: Add to an existing vault
Copy `WIKI.md` from this repo into your vault root. Then paste into Claude:
```
Read WIKI.md in this project. Then:
1. Check if Obsidian is installed. If not, install it.
2. Check if the Local REST API plugin is running on port 27124.
3. Configure the MCP server.
4. Ask me ONE question: "What is this vault for?"
Then scaffold the full wiki structure.
```
---
## First Steps
### 1. Scaffold the vault
Type `/wiki` in Claude Code. Claude will:
- Detect your vault mode (website, GitHub, business, personal, research, or book/course)
- Create the folder structure and core wiki pages
- Set up `wiki/index.md`, `wiki/hot.md`, `wiki/log.md`, and `wiki/overview.md`
### 2. Drop your first source
Put any document into `.raw/`:
- PDFs, markdown files, transcripts, articles, URLs
Tell Claude: `ingest [filename]`
Claude reads the source and creates 8–15 cross-referenced wiki pages.
### 3. Ask questions
```
what do you know about [topic]?
```
Claude reads the hot cache, scans the index, drills into relevant pages, and gives a synthesized answer, citing specific wiki pages, not training data.
---
## Commands Reference
| Command | What Claude does |
|---------|-----------------|
| `/wiki` | Setup check, scaffold, or continue where you left off |
| `ingest [file]` | Read source, create 8–15 wiki pages, update index and log |
| `ingest all of these` | Batch process multiple sources, then cross-reference |
| `what do you know about X?` | Read index → relevant pages → synthesize answer |
| `/save` | File the current conversation as a wiki note |
| `/save [name]` | Save with a specific title |
| `/autoresearch [topic]` | Autonomous research loop: search, fetch, synthesize, file |
| `/canvas` | Open or create a visual canvas |
| `/canvas add image [path]` | Add an image to the canvas |
| `/canvas add text [content]` | Add a markdown text card |
| `/canvas add pdf [path]` | Add a PDF document |
| `/canvas add note [page]` | Pin a wiki page as a linked card |
| `lint the wiki` | Health check: orphans, dead links, gaps |
| `update hot cache` | Refresh `hot.md` with latest context summary |
---
## Plugins (pre-installed)
Enable in **Settings → Community Plugins**:
| Plugin | Purpose |
|--------|---------|
| **Calendar** | Right-sidebar calendar with word count and task dots |
| **Thino** | Quick memo capture panel |
| **Excalidraw** | Freehand drawing, image annotation |
| **Banners** | Header images via `banner:` frontmatter |
Also install from Community Plugins:
| Plugin | Purpose |
|--------|---------|
| **Dataview** | Powers the dashboard queries |
| **Templater** | Auto-fills frontmatter from templates |
| **Obsidian Git** | Auto-commits vault every 15 minutes |
---
## CSS Snippets
Three snippets are auto-enabled by `setup-vault.sh`:
| Snippet | Effect |
|---------|--------|
| `vault-colors` | Color-codes wiki folders in the file explorer |
| `ITS-Dataview-Cards` | Turns Dataview queries into visual card grids |
| `ITS-Image-Adjustments` | Fine-grained image sizing; append `\|100` to embeds |
---
## Six Wiki Modes
| Mode | Use when |
|------|---------|
| **A: Website** | Sitemap, content audit, SEO wiki |
| **B: GitHub** | Codebase map, architecture wiki |
| **C: Business** | Project wiki, competitive intelligence |
| **D: Personal** | Second brain, goals, journal synthesis |
| **E: Research** | Papers, concepts, thesis |
| **F: Book/Course** | Chapter tracker, course notes |
Modes can be combined.
---
## MCP Setup (Optional)
MCP lets Claude read and write vault notes directly without copy-paste.
**Option A: REST API**
1. Install the **Local REST API** plugin in Obsidian
2. Copy your API key
3. Run:
```bash
claude mcp add-json obsidian-vault '{
"type": "stdio",
"command": "uvx",
"args": ["mcp-obsidian"],
"env": {
"OBSIDIAN_API_KEY": "your-key",
"OBSIDIAN_HOST": "127.0.0.1",
"OBSIDIAN_PORT": "27124",
"NODE_TLS_REJECT_UNAUTHORIZED": "0"
}
}' --scope user
```
**Option B: Filesystem (no plugin needed)**
```bash
claude mcp add-json obsidian-vault '{
"type": "stdio",
"command": "npx",
"args": ["-y", "@bitbonsai/mcpvault@latest", "/path/to/your/vault"]
}' --scope user
```
---
## Troubleshooting
| Problem | Fix |
|---------|-----|
| `/wiki` says "not found" | Make sure `claude-obsidian` plugin is enabled: `claude plugin list` |
| Graph colors reset after closing Obsidian | Open Graph view → gear → Color groups → re-add once. Permanent after that. |
| Excalidraw not loading | Run `bash bin/setup-vault.sh` to download `main.js` (8MB, not in git) |
| Dashboard shows no results | Install the **Dataview** plugin from Community Plugins |
| Hot cache not loading at session start | Check hooks: `claude hooks list`; SessionStart hook should be present |
---
## Cross-Project Power Move
Point any Claude Code project at this vault. Add to that project's `CLAUDE.md`:
```markdown
## Wiki Knowledge Base
Path: ~/path/to/claude-obsidian
When you need context not in this project:
1. Read wiki/hot.md first (recent context cache)
2. If not enough, read wiki/index.md
3. If you need domain details, read the relevant wiki page
Do NOT read the wiki for general coding questions.
```
Your executive assistant, coding projects, and content workflows all draw from the same knowledge base.
---
## Support
- **GitHub (public canonical)**: [github.com/AgriciDaniel/claude-obsidian](https://github.com/AgriciDaniel/claude-obsidian)
- **Issues**: [github.com/AgriciDaniel/claude-obsidian/issues](https://github.com/AgriciDaniel/claude-obsidian/issues)
- **Community early-access (Pro)**: [AI Marketing Hub org](https://github.com/AI-Marketing-Hub) · [Skool community](https://www.skool.com/ai-marketing-hub-pro)
---
*Built by [AgriciDaniel](https://github.com/AgriciDaniel) / AI Marketing Hub*
*Based on Andrej Karpathy's LLM Wiki pattern*
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# Methodology Modes Guide — v1.8.0
**Status:** v1.8.0 GA (2026-05-17)
**Scope:** picks an organizational style for your vault and routes new pages accordingly.
**Origin:** closes priority gap 5 from the May 2026 compass artifact.
---
## TL;DR
Pick a mode that matches how YOU think:
| You think in... | Pick |
|---|---|
| Topic clusters + navigation by following links | **LYT** |
| Active projects vs ongoing responsibilities vs reference material | **PARA** |
| Atomic claims with unique IDs and dense linking | **Zettelkasten** |
| No methodology / want v1.7 default | **Generic** |
```bash
bash bin/setup-mode.sh # interactive
bash bin/setup-mode.sh --mode lyt # non-interactive
```
After picking, `wiki-ingest`, `save`, and `autoresearch` consult the mode before deciding where to file new pages. Existing files are NOT moved; the mode only affects future filing.
---
## Why methodology modes exist
The May 2026 compass artifact identified 5 priority gaps. claude-obsidian v1.7 closed 4 of them (substrate alignment, default transport, hybrid retrieval, multi-writer safety) and deferred the 5th — methodology support — to v1.8.
The audit §9 axis evaluation called methodology support a **TIE** in May 2026: nobody else in the Claude+Obsidian space ships it as a first-class skill. Ideaverse Pro 2.0 ($200 paid vault) ships LYT as an opinionated structure but it's a vault, not a skill set. PARA, Zettelkasten, and mode-aware routing are entirely unserved.
v1.8.0 closes that gap. After this release, claude-obsidian is **#1 on 5 of 7 axes** per the compass framework (compounding wiki, multi-writer safety, retrieval architecture, license openness, methodology support). The remaining 2 (GUI ergonomics, derivative outputs) require larger releases (v2.5+ for GUI, v2.0 for derive).
---
## The four modes
### Generic (default)
**Philosophy:** no methodology imposed. Same as v1.6/v1.7.
**Filing convention:**
- `wiki/sources/<slug>.md` — ingested source documents
- `wiki/entities/<Name>.md` — people, orgs, products (capitalization preserved)
- `wiki/concepts/<Name>.md` — concepts and frameworks
- `wiki/sessions/<date>-<topic>.md` — session notes from `/save`
**When to use:**
- You're migrating from v1.7 and want zero behavior change
- You don't want to commit to a methodology yet
- You have your own organizational instincts and want minimal opinion
**Pros:** zero learning curve; matches v1.7 muscle memory; flexible.
**Cons:** no opinion to lean on; can sprawl in large vaults.
---
### LYT (Linking Your Thinking — Nick Milo)
**Philosophy:** the organizational primitive is the **MOC** (Map of Content). Atomic notes flat under one folder; MOCs link into clusters of notes. You navigate by following links, not by browsing folders.
**Filing convention:**
- `wiki/mocs/<topic>-moc.md` — Map of Content for a topic cluster
- `wiki/notes/<atomic-note>.md` — all atomic notes flat (no subfolders)
- Every atomic note has at least one MOC in its frontmatter `mocs:` field
- New ingests land in `wiki/notes/`; consumer skill also updates the relevant MOC
**Templates** (under `skills/wiki-mode/templates/lyt/`):
- `moc-template.md` — MOC scaffolding with core-notes / adjacent-MOCs / open-questions sections
- `atomic-template.md` — atomic note with MOC backlinks
**When to use:**
- Mid-to-large knowledge bases (>100 notes)
- You think in conceptual clusters and knowledge graphs
- You're an LYT practitioner or want to be one
**Pros:** scales beautifully; navigation gets richer with growth; explicit knowledge structure.
**Cons:** discipline of always-update-MOCs; flat notes folder can feel chaotic without good search.
---
### PARA (Tiago Forte)
**Philosophy:** organize by **actionability**, not topic. Active work in Projects (with deadline + outcome), ongoing responsibilities in Areas (no deadline), reference material in Resources (by topic), completed/inactive work in Archives.
**Filing convention:**
- `wiki/projects/<project-name>/<note>.md` — active projects
- `wiki/projects/inbox/<note>.md` — new ingests + session notes land here for triage
- `wiki/areas/<area-name>/<note>.md` — ongoing responsibilities
- `wiki/resources/<topic>/<note>.md` — reference material
- `wiki/resources/incoming/<note>.md` — new sources land here for topical sorting
- `wiki/resources/people/<Name>.md` — entity pages
- `wiki/resources/concepts/<Name>.md` — concept pages
- `wiki/archives/<year>/<note>.md` — completed projects, sunsetted areas
**Templates** (under `skills/wiki-mode/templates/para/`):
- `project-template.md` — project with status / deadline / outcome / next-action
- `area-template.md` — area with scope / standards / review cadence
- `resource-template.md` — reference material with topic + sources
**When to use:**
- Workflow-heavy users
- Knowledge workers managing many projects
- GTD-adjacent practitioners
- Anyone who has read Tiago Forte's "Building a Second Brain"
**Pros:** explicit project lifecycle; clear separation of active vs reference; matches how knowledge workers actually operate.
**Cons:** requires periodic review to move completed projects → archives; "incoming" buckets need to be processed.
---
### Zettelkasten (Niklas Luhmann's slip-box)
**Philosophy:** atomic notes, unique IDs, dense bidirectional linking. No folders. Every note answers exactly one idea. Notes find each other by ID references.
**Filing convention:**
- `wiki/<YYYYMMDDHHMMSSffffff>-<slug>.md` — flat under wiki/, timestamped IDs (20 digits = date + microseconds, collision-resistant)
- Every note has `id:`, `parent_id:` (optional), `child_ids:` (optional) in frontmatter
- No subdirectories; the wiki/ root is the whole vault
- All organization is via `parent_id` / `child_ids` / `[[ID]]` references in note bodies
**Templates** (under `skills/wiki-mode/templates/zettel/`):
- `atomic-template.md` — atomic claim with parent/child IDs + reasoning + sources
**When to use:**
- Academics and researchers
- Long-term thinkers building permanent knowledge artifacts
- Anyone who's read "How to Take Smart Notes" by Sönke Ahrens
- High-discipline, small-filing-surface preference
**Pros:** maximum link density; encourages atomic thinking; ages well over decades.
**Cons:** steepest discipline curve; flat file list is intimidating without good search; ID-based reference is less mnemonic than name-based.
---
## How modes interact with other skills
The integration is **automatic** — once you set a mode, `wiki-ingest`, `save`, and `autoresearch` consult it on every new page. You never have to think about it.
| Skill | What it does | How mode affects it |
|---|---|---|
| `wiki-ingest` | files new source/entity/concept pages | router determines destination folder per mode |
| `save` | files session notes from the current conversation | router determines `wiki/sessions/` (generic), `wiki/notes/` + MOC update (LYT), `wiki/projects/inbox/` (PARA), or `wiki/<ID>-session-...` (Zettel) |
| `autoresearch` | files synthesis page after a research loop | router determines `wiki/concepts/` (generic), `wiki/notes/` + topic MOC (LYT), `wiki/resources/<topic>/` (PARA), or `wiki/<ID>-...` (Zettel) |
The router (`scripts/wiki-mode.py route <type> "<name>"`) is the single source of truth. Skills don't compute paths themselves; they call the router and use what it returns.
---
## Switching modes later
Switching modes is **safe but does NOT auto-migrate**:
1. Run `bash bin/setup-mode.sh` (or `--mode <new-mode>` non-interactively)
2. The new mode is written to `.vault-meta/mode.json`
3. Existing files remain in their original locations and continue to work
4. New files file per the new mode
5. (Optional manual step) Use your file manager or `git mv` to migrate existing files to the new structure
**Why no auto-migration:** the wiki contains your thinking. Auto-rewriting paths could break wikilinks, lose data, or surprise you. Manual migration forces explicit decisions about what fits the new methodology vs what stays in its current home.
**Specifically for LYT migration:** after switching to LYT, run `lint the wiki` (skill: wiki-lint) to identify orphan pages that would benefit from MOC inclusion.
---
## Mode config file
`.vault-meta/mode.json` is the active mode declaration. It's **gitignored by default** — the file is treated as host-specific runtime config. To commit your mode choice across machines / collaborators:
```bash
git add -f .vault-meta/mode.json
git commit -m "chore: declare vault mode as <mode>"
```
The file schema:
```json
{
"schema_version": 1,
"mode": "lyt|para|zettelkasten|generic",
"configured_at": "2026-05-17T00:00:00Z",
"config": {
"lyt": {"moc_folder": "wiki/mocs/", "notes_folder": "wiki/notes/"},
"para": {"projects_folder": "...", "areas_folder": "...", "resources_folder": "...", "archives_folder": "..."},
"zettelkasten": {"id_format": "YYYYMMDDHHMMSSffffff", "no_folders": true, "root_folder": "wiki/"},
"generic": {"sources_folder": "wiki/sources/", "entities_folder": "wiki/entities/", "concepts_folder": "wiki/concepts/", "sessions_folder": "wiki/sessions/"}
}
}
```
The `config` block always includes all 4 modes. The active mode is named by `mode`. Per-mode folder paths can be overridden in your `mode.json` if you want non-default conventions.
---
## When NOT to use mode-awareness
- **Tiny vaults** (<20 notes): the overhead of organization isn't justified yet. Stick with generic.
- **Vaults you didn't choose to organize**: if you don't care about methodology, don't pick one. Generic is honest.
- **Cross-project shared vaults** (per global CLAUDE.md `/save` convention): the personal vault at `~/Documents/Obsidian Vault/` has its own organizational choices; the project's mode-router only applies to the project's own `wiki/`.
---
## Roadmap from here
v1.8.0 closes priority gap 5. The compass artifact's full picture:
| Axis (per audit §9) | v1.7.2 status | v1.8.0 status | Path to LEAD |
|---|---|---|---|
| Compounding wiki primitive | #1 | #1 | ✓ |
| Multi-writer safety | #1 | #1 | ✓ |
| Retrieval architecture (free tier) | #1 | #1 | ✓ |
| License / openness | #1 | #1 | ✓ |
| **Methodology support** | TIE | **#1** ← v1.8.0 closes | ✓ |
| Derivative outputs (audio/video/quiz) | NO | NO | v2.0 (wiki-derive) |
| GUI / install ergonomics | NO | NO | v2.5+ (Community Plugin fork) |
After v1.8.0: **#1 on 5 of 7 axes per compass framework**. The remaining 2 axes require multi-release effort:
- **v1.9** — multimodal ingest (YouTube / PDF / EPUB / image OCR)
- **v2.0** — `wiki-derive` skill: audio overviews, quiz generation, study guides, mindmap synthesis (NotebookLM parity)
- **v2.5+** — Community Plugin GUI shell (mainstream Obsidian user reach)
---
## Cross-reference
- [`skills/wiki-mode/SKILL.md`](../skills/wiki-mode/SKILL.md) — the skill itself
- [`scripts/wiki-mode.py`](../scripts/wiki-mode.py) — router + config helper
- [`bin/setup-mode.sh`](../bin/setup-mode.sh) — interactive setup
- [`tests/test_wiki_mode.py`](../tests/test_wiki_mode.py) — hermetic test suite (15 assertions)
- [`docs/compound-vault-guide.md`](compound-vault-guide.md) — v1.7 omnibus that v1.8 builds on
- v1.7.0 audit §9 axis 6: [`docs/audits/v1.7.0-audit-2026-05-17.md`](audits/v1.7.0-audit-2026-05-17.md)
docs/releases/v1.6.0.md
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> DragonScale is now a four-mechanism, opt-in memory layer for LLM wiki vaults.
![DragonScale Memory mechanism overview](https://raw.githubusercontent.com/AgriciDaniel/claude-obsidian/main/wiki/meta/dragonscale-mechanism-overview.png)
## TL;DR
- Shipped: DragonScale now has fold rollups, deterministic page addresses, semantic tiling lint, and boundary-first autoresearch.
- Gated on: `bash bin/setup-dragonscale.sh`, plus local dependencies per mechanism.
- Did not ship: fold-of-folds, calibrated tiling thresholds, hosted mode, or multi-vault rollup.
## Same-day release sequence
The plugin version is `1.6.0` and the annotated tag `v1.6.0` points at the release commit on `main`.
The narrative below includes `1.5.0`, `1.5.1`, and `1.6.0` because 2026-04-24 bundled three local release states into one cycle.
`1.5.0` was Phase 3.5.
It hardened the DragonScale base.
It added the installer, test harness, changelog, Makefile targets, and opt-in wiring for the first three mechanisms.
It also synced plugin metadata to `1.5.0`.
`1.5.1` was Phase 3.6.
It fixed five narrow issues before Phase 4.
Those fixes covered tiling report path confinement, rollout baseline date, AGENTS wording, `.raw/` manifest wording, and install-guide version drift.
`1.6.0` was Phase 4.
It shipped Mechanism 4: boundary-first autoresearch.
It added `scripts/boundary-score.py`, wired no-topic `/autoresearch` into frontier suggestions, added boundary-score tests, and bumped the DragonScale spec to v0.4.
## Four mechanisms
<!-- overview diagram rendered at the top of the page. -->
### 1. Fold operator
What:
extractive rollups of `wiki/log.md` entries into fold pages under `wiki/folds/`.
Invoke:
ask `fold the log, dry-run k=3`, then `fold the log, commit k=3` if the output is right.
Skip:
skip when the log has no coherent batch, or when you want deletion-based compaction.
Folds summarize.
They do not garbage collect.
Status:
shipped in `1.5.0`.
First real run:
`wiki/folds/fold-k3-from-2026-04-23-to-2026-04-24-n8.md`.
Observed output:
115 lines.
8 children.
Flat extractive fold.
### 2. Deterministic page addresses
What:
stable `address: c-NNNNNN` frontmatter for new non-meta wiki pages.
Invoke:
run `./scripts/allocate-address.sh` directly, or let `wiki-ingest` assign addresses after DragonScale setup.
Skip:
skip when you do not need stable page IDs, or when more than one writer may assign addresses at the same time.
Status:
shipped in `1.5.0`.
Format:
`c-000042`.
Important limit:
this is a creation-order counter.
It is not a content hash.
Validation run:
counter advanced from 2 to 3.
It returned `c-000002`.
The unassigned reservation gap is acceptable under the spec.
### 3. Semantic tiling lint
What:
embedding-based duplicate-page detection for the wiki.
Invoke:
run `python3 ./scripts/tiling-check.py --peek` for readiness, or `python3 ./scripts/tiling-check.py --report wiki/meta/tiling-report-YYYY-MM-DD.md` for a saved report.
Skip:
skip when `ollama` or `nomic-embed-text` is unavailable, or when uncalibrated review bands would create more noise than signal.
Status:
shipped in `1.5.0`.
Default model:
local `nomic-embed-text` through `ollama`.
Default bands:
`>= 0.90` error.
`0.80` to `0.90` review.
Below `0.80` pass.
Important limit:
the defaults are seed values.
They are not calibrated to this vault.
First full report:
`wiki/meta/tiling-report-2026-04-24.md`.
### 4. Boundary-first autoresearch
What:
frontier scoring for wiki pages, used as candidate selection for no-topic `/autoresearch`.
Invoke:
run `/autoresearch` with no topic in a DragonScale-enabled vault, or run `python3 ./scripts/boundary-score.py --json --top 5`.
Skip:
skip when you want explicit topic control only, or when you want DragonScale limited to pure memory operations.
Status:
shipped in `1.6.0`.
Formula:
`boundary_score(p) = (out_degree(p) - in_degree(p)) * exp(-days_since_updated / 30)`.
What it does:
finds pages that point outward, receive few inbound links, and are still recent enough to be useful.
What it is not:
it is not pure memory.
It is agenda control.
The user still chooses the topic.
First run artifact:
`wiki/meta/boundary-frontier-2026-04-24.md`.
Top frontier facts:
22 scoreable pages.
7 positive-score pages reported.
Top score was `4.693`.
`DragonScale Memory` scored `4.000`.
## The dragon curve, briefly
The Heighway dragon is built by paperfolding recursion.
Each construction step folds a turn sequence into a larger self-similar sequence.
The turn sequence is the regular paperfolding sequence, OEIS A014577.
See [Dragon curve](https://en.wikipedia.org/wiki/Dragon_curve).
Its boundary has fractal dimension about `1.5236`.
That number is useful here as orientation, not as proof.
It says the boundary is not a simple line and not a filled plane.
It is structured frontier.
That makes it a good analogy for a memory layer.
Recursive structure suggests hierarchical rollup.
Self-similar boundary suggests frontier-first agenda.
But this is analogy, not derivation.
DragonScale does not prove optimal memory behavior from curve geometry.
## Enablement
Run:
```bash
bash bin/setup-dragonscale.sh
```
Prereqs:
base vault setup first, `flock` for allocator and tiling locks, `python3` for Mechanisms 3 and 4, and local `ollama` plus `nomic-embed-text` for Mechanism 3.
Guide:
[docs/dragonscale-guide.md](../dragonscale-guide.md).
## Validation
![Six-test validation flow](https://raw.githubusercontent.com/AgriciDaniel/claude-obsidian/main/wiki/meta/dragonscale-6-test-flow.png)
Validation date:
2026-04-24.
Source:
`wiki/log.md`, entry `DragonScale end-to-end validation pass (Teams, 6 tests)`.
Result:
the six-test menu passed.
`make test` stayed green throughout.
T0:
pulled `nomic-embed-text` for local embeddings.
Observed:
274 MB.
15 seconds wall time.
T1:
ran Mechanism 1 dry-run with `k=3`.
Observed:
dry-run OK.
8 children.
No em dashes in generated fold content.
T2:
ran Mechanism 2 real allocation.
Observed:
counter advanced from 2 to 3.
Returned `c-000002`.
The address was an unassigned reservation.
Gap accepted by spec.
T3:
ran Mechanism 3 full tiling with model present.
Observed:
41 pages scanned.
21 pages embedded.
20 pages skipped.
0 errors at `>= 0.90`.
15 review pairs in `0.80` to `0.90`.
Top review pair:
`0.8822` for `Compounding Knowledge` and `LLM Wiki Pattern`.
Interpretation:
legitimate semantic neighbor.
Not an automatic merge.
Report:
`wiki/meta/tiling-report-2026-04-24.md`.
T4:
ran Mechanism 1 commit.
Observed:
first real fold committed.
115 lines.
8 children.
Flat extractive fold.
Fold:
`wiki/folds/fold-k3-from-2026-04-23-to-2026-04-24-n8.md`.
Why it matters:
it flips the old status from dry-run only to one committed fold in this vault.
Closeout test status:
`make test` passed.
Closeout counts:
12 shell assertions for address allocation.
18 Python assertions for tiling.
44 Python assertions for boundary scoring.
Zero `ollama` dependency.
T6:
ran Mechanism 4 no-topic autoresearch.
Observed:
selected `How does the LLM Wiki pattern work?`.
Score `1.7022`.
It was candidate number 3 after skipping the top source page and top self-reference.
Fetches:
6 web fetches.
Inputs included:
Karpathy gist.
RAG paper `arXiv:2005.11401`.
MemGPT paper `arXiv:2310.08560`.
Obsidian docs.
Output:
3 new concept pages filed.
Each included Primary Sources.
New concept pages:
- `wiki/concepts/Persistent Wiki Artifact.md`
- `wiki/concepts/Source-First Synthesis.md`
- `wiki/concepts/Query-Time Retrieval.md`
Integration:
the new concepts were added to `wiki/index.md` and `wiki/concepts/_index.md`.
They extend `How does the LLM Wiki pattern work?`.
They cross-reference `LLM Wiki Pattern`.
![Boundary-first autoresearch: frontier picked, pages filed](https://raw.githubusercontent.com/AgriciDaniel/claude-obsidian/main/wiki/meta/dragonscale-frontier-graph.png)
## What is not in v1.6.0
- No fold-of-folds.
- No hierarchical level stacking beyond one flat committed fold.
- No automatic deletion or compaction of child pages.
- No calibrated M3 thresholds.
- No literature-backed M3 bands for this specific vault.
- No automatic merging from tiling results.
- No pure-memory claim for M4.
- No hidden topic choice in M4.
- No hosted or managed mode.
- No multi-vault fold rollup.
- No multi-writer address-assignment guarantee.
- No alias-aware full Obsidian wikilink resolver in boundary scoring.
- No persistent boundary-score cache.
- No automatic autoresearch trigger.
## Upgrade from v1.4.x
This is non-breaking for base users.
Upgrade path:
1. Pull `main`.
2. Reinstall as a plugin if your agent setup requires it.
3. Keep using the normal v1.4.x wiki workflow if you do not want DragonScale.
4. Opt into DragonScale only when ready:
```bash
bash bin/setup-dragonscale.sh
```
If you do not opt in, nothing changes from your v1.4.x workflow.
DragonScale is feature-detected.
`wiki-ingest`, `wiki-lint`, and `/autoresearch` fall back when the setup state or helper dependencies are absent.
## Attribution
Diagrams in this release note are original SVGs under the repo license (MIT).
The dragon curve and paperfolding references are text-only. For images and construction history, see the Wikipedia article linked above.
Fonts used in the SVGs: Space Grotesk (SIL Open Font License), with system-ui fallback.
## Credits
- Karpathy LLM Wiki pattern.
- Heighway paperfolding and the dragon curve analogy.
- Codex sub-agent delegation for the release validation and review loop.
hooks/README.md
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# claude-obsidian Hooks
Plugin hooks for the claude-obsidian wiki vault. All hooks are defined in `hooks.json`.
## Events
| Event | Type | Purpose |
|---|---|---|
| `SessionStart` | command + prompt | Loads `wiki/hot.md` into context. Command type runs `[ -f wiki/hot.md ] && cat wiki/hot.md` as the canonical safety check (works for non-vault sessions without erroring). Prompt type complements with semantic context restoration. Matcher: `startup\|resume`. |
| `PostCompact` | prompt | Re-loads `wiki/hot.md` after context compaction. Hook-injected context does NOT survive compaction (only `CLAUDE.md` does), so this hook restores the hot cache mid-session. |
| `PostToolUse` | command | Auto-commits any wiki/ or .raw/ changes after Write or Edit tool calls. Guarded by `[ -d .git ]` so it never errors in non-git directories, and by `git diff --cached --quiet` so it never creates empty commits. |
| `Stop` | prompt | Updates `wiki/hot.md` at the end of every Claude response with a brief summary of what changed. |
## Known Issue: Plugin Hooks STDOUT Bug
`anthropics/claude-code#10875` documents that **plugin hook STDOUT may not be captured** by Claude Code, while identical inline hooks in `settings.json` work correctly.
**Impact**: If this bug is active in your Claude Code version, the prompt-type SessionStart and PostCompact hooks may not inject context as expected.
**Workaround**: The command-type SessionStart hook (`cat wiki/hot.md`) is the canonical safety check. It relies on STDOUT capture for context injection, so test against this issue if hot cache restoration fails. As a fallback, copy the hook config from `hooks.json` into your user-level `~/.claude/settings.json` instead of relying on plugin hooks.
**Test for the bug**: After installing the plugin, open a fresh Claude Code session in a directory containing a populated `wiki/hot.md`. Ask Claude "what's in the hot cache?". If Claude has no idea, the STDOUT bug is active in your version.
## Non-Vault Sessions
The SessionStart command hook uses `[ -f wiki/hot.md ] && cat wiki/hot.md || true` so it always exits 0, even when no vault is present. This makes the plugin safe to install globally without breaking non-vault Claude Code sessions.
hooks/hooks.json
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{
"hooks": {
"SessionStart": [
{
"matcher": "startup|resume",
"hooks": [
{
"type": "command",
"command": "[ -f wiki/hot.md ] && cat wiki/hot.md || true"
},
{
"type": "command",
"command": "[ -x scripts/wiki-lock.sh ] && bash scripts/wiki-lock.sh clear-stale --max-age 3600 >/dev/null 2>&1 || true"
},
{
"type": "prompt",
"prompt": "If a vault is configured for this session (check CLAUDE.md for VAULT_PATH or a wiki/ folder in the current directory), silently read wiki/hot.md to restore recent context. If wiki/hot.md does not exist, do nothing. This is a non-vault session. Do not announce this. Do not report what you read. Just have the context available."
}
]
}
],
"PostCompact": [
{
"matcher": "",
"hooks": [
{
"type": "prompt",
"prompt": "Hook-injected context does not survive context compaction. If wiki/hot.md exists in the current directory, silently re-read it now to restore the hot cache. Do not announce this."
}
]
}
],
"PostToolUse": [
{
"matcher": "Write|Edit",
"hooks": [
{
"type": "command",
"command": "[ -d .git ] || exit 0; [ -f .vault-meta/auto-commit.disabled ] && exit 0; if [ -x scripts/wiki-lock.sh ]; then LOCK_LIST=$(bash scripts/wiki-lock.sh list 2>/dev/null); LOCK_RC=$?; if [ \"$LOCK_RC\" != \"0\" ]; then mkdir -p .vault-meta 2>/dev/null; printf '%s wiki-lock list failed rc=%s; deferred auto-commit\\n' \"$(date '+%Y-%m-%dT%H:%M:%SZ')\" \"$LOCK_RC\" >> .vault-meta/hook.log 2>/dev/null; exit 0; fi; if [ -n \"$LOCK_LIST\" ]; then exit 0; fi; fi; git add -- wiki/ .raw/ .vault-meta/ 2>/dev/null && (git diff --cached --quiet -- wiki/ .raw/ .vault-meta/ || git commit -m \"wiki: auto-commit $(date '+%Y-%m-%d %H:%M')\" -- wiki/ .raw/ .vault-meta/ 2>/dev/null) || true"
}
]
}
],
"Stop": [
{
"matcher": "",
"hooks": [
{
"type": "command",
"command": "cd \"$PWD\" && [ -d wiki ] && [ -d .git ] && git diff --name-only HEAD 2>/dev/null | grep -q '^wiki/' && echo 'WIKI_CHANGED: Wiki pages were modified this session. Please update wiki/hot.md with a brief summary of what changed (under 500 words). Use the hot cache format: Last Updated, Key Recent Facts, Recent Changes, Active Threads. Keep it factual. Overwrite the file completely. It is a cache, not a journal.' || true"
}
]
}
]
}
}
scripts/allocate-address.sh
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#!/usr/bin/env bash
# allocate-address.sh — atomic creation-order address allocation for the vault.
#
# Reserves the next address of the form c-NNNNNN and increments the counter
# under an exclusive flock. On missing counter file, recovers by scanning the
# vault for the highest existing c-NNNNNN in page frontmatter and resuming from
# max+1. Never silently resets to 1 in a non-empty vault.
#
# Usage:
# ./scripts/allocate-address.sh # prints the reserved address (e.g. c-000042) to stdout
# ./scripts/allocate-address.sh --peek # prints the next value without incrementing
# ./scripts/allocate-address.sh --rebuild # recomputes counter from max observed and exits
#
# Exit codes:
# 0 — success
# 1 — lock acquisition failed (another writer is holding the lock)
# 2 — vault-meta directory missing and cannot be created
# 3 — counter value corrupt or non-numeric
set -euo pipefail
VAULT_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
COUNTER_FILE="${VAULT_ROOT}/.vault-meta/address-counter.txt"
LOCK_FILE="${VAULT_ROOT}/.vault-meta/.address.lock"
WIKI_DIR="${VAULT_ROOT}/wiki"
MODE="${1:-allocate}"
mkdir -p "$(dirname "$COUNTER_FILE")" || {
echo "ERR: cannot create .vault-meta/" >&2
exit 2
}
# Acquire exclusive lock with 5-second timeout. Release automatically on scope exit.
exec 9>"$LOCK_FILE"
if ! flock -x -w 5 9; then
echo "ERR: could not acquire address allocator lock within 5s" >&2
exit 1
fi
scan_max_c_address() {
# Emit the largest NNNNNN from "address: c-NNNNNN" lines that appear inside
# the FIRST YAML frontmatter block of each wiki .md file. Code-block examples
# and body prose are excluded. Returns 0 if none found.
if [ ! -d "$WIKI_DIR" ]; then
echo 0
return
fi
find "$WIKI_DIR" -type f -name '*.md' -print0 2>/dev/null \
| xargs -0 awk '
FNR == 1 { state = "pre"; next_is_fm = ($0 == "---") ? 1 : 0 }
FNR == 1 && $0 == "---" { state = "fm"; next }
state == "fm" && $0 == "---" { state = "body"; nextfile }
state == "fm" && match($0, /^address:[[:space:]]+c-[0-9]{6}[[:space:]]*$/) {
if (match($0, /c-[0-9]{6}/)) {
print substr($0, RSTART, RLENGTH)
}
}
' 2>/dev/null \
| sed 's/^c-0*//;s/^$/0/' \
| sort -n \
| tail -1 \
| awk 'BEGIN{n=0} {n=$0} END{print (n+0)}'
}
read_or_recover_counter() {
if [ ! -f "$COUNTER_FILE" ]; then
local max_c
max_c="$(scan_max_c_address)"
echo $((max_c + 1)) > "$COUNTER_FILE"
echo "INFO: counter file missing; recovered from vault scan, set to $((max_c + 1))" >&2
fi
local raw
raw="$(cat "$COUNTER_FILE")"
if ! [[ "$raw" =~ ^[0-9]+$ ]]; then
echo "ERR: counter file content is not a positive integer: $raw" >&2
exit 3
fi
echo "$raw"
}
case "$MODE" in
--peek)
read_or_recover_counter
;;
--rebuild)
max_c="$(scan_max_c_address)"
echo $((max_c + 1)) > "$COUNTER_FILE"
echo "Counter rebuilt: next = $((max_c + 1))"
;;
allocate|"")
current="$(read_or_recover_counter)"
next=$((current + 1))
echo "$next" > "$COUNTER_FILE"
printf 'c-%06d\n' "$current"
;;
*)
echo "ERR: unknown mode: $MODE" >&2
echo "Usage: $0 [allocate|--peek|--rebuild]" >&2
exit 3
;;
esac
scripts/baseline-v16.py
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#!/usr/bin/env python3
"""baseline-v16.py — simulate the v1.6 hot→index→drill retrieval chain.
Exists ONLY for benchmarking v1.7's hybrid retrieval against the legacy
v1.6 behavior. Not used by any v1.7 skill; not feature-gated; not part of
the regular vault workflow.
The v1.6 query path (per skills/wiki-query/SKILL.md before v1.7):
1. Read wiki/hot.md (always; quick context)
2. Read wiki/index.md (scan for descriptions matching query terms)
3. Read top-N pages cited in the index whose entries best match query
4. Caller synthesizes answer
This script approximates that path by:
1. Tokenizing the query (same stopword-filtered ASCII tokenizer as bm25-index.py)
2. Scoring each *.md page in wiki/ by the count of distinct query terms it contains
(case-insensitive substring on the full file body; no semantic matching)
3. Returning top-K pages by score, with ties broken by:
a. Presence in hot.md (boost +5)
b. Presence in index.md (boost +3)
c. Total raw term-occurrence count
The simulation is intentionally simple — it represents what a human or a
basic agent does when reading hot/index "by hand" without any retrieval
infrastructure. Anything fancier would not be a fair v1.6 baseline.
Usage:
baseline-v16.py "your query" [--top 5]
baseline-v16.py "query" --top 5 --json # output as JSON (default: text)
Exit codes:
0 — success
2 — usage error
3 — wiki directory missing
"""
import argparse
import json
import re
import sys
from collections import Counter
from pathlib import Path
VAULT_ROOT = Path(__file__).resolve().parent.parent
WIKI_DIR = VAULT_ROOT / "wiki"
HOT_PATH = WIKI_DIR / "hot.md"
INDEX_PATH = WIKI_DIR / "index.md"
# Mirror bm25-index.py's tokenizer + stopword list so comparisons are fair.
STOPWORDS = frozenset("""
a an and are as at be by for from has have he her him his i if in is it its
of on or that the their them they this to was were will with you your
""".split())
# Mirrors bm25-index.py's Unicode-aware tokenizer (v1.7.2; closes M2).
TOKEN_RE = re.compile(r"\w[\w'\-]*", re.UNICODE)
HOT_BOOST = 5.0
INDEX_BOOST = 3.0
EXIT_OK = 0
EXIT_USAGE = 2
EXIT_NO_WIKI = 3
def tokenize(text):
return [t.lower() for t in TOKEN_RE.findall(text)
if t.lower() not in STOPWORDS and len(t) > 1]
def page_paths():
if not WIKI_DIR.is_dir():
print(f"ERR: no wiki directory at {WIKI_DIR}", file=sys.stderr)
sys.exit(EXIT_NO_WIKI)
return sorted(p for p in WIKI_DIR.rglob("*.md")
if not any(part.startswith(".") for part in p.parts))
def score_page(page_path, query_terms_set, query_terms_counter):
"""Score by distinct-query-term-presence + boost if cited in hot/index.
Returns (score, distinct_matches, total_occurrences).
"""
try:
body = page_path.read_text(encoding="utf-8", errors="replace").lower()
except OSError:
return (0.0, 0, 0)
distinct = sum(1 for term in query_terms_set if term in body)
total = sum(body.count(term) for term in query_terms_set)
score = float(distinct) + 0.01 * total # distinct dominates; total is tiebreak
# Hot-cache boost: if the page is referenced by name in hot.md
if HOT_PATH.is_file():
try:
hot_body = HOT_PATH.read_text(encoding="utf-8", errors="replace")
page_stem = page_path.stem
if page_stem in hot_body or str(page_path.relative_to(VAULT_ROOT)) in hot_body:
score += HOT_BOOST
except OSError:
pass
# Index boost: page is cited in index.md
if INDEX_PATH.is_file():
try:
index_body = INDEX_PATH.read_text(encoding="utf-8", errors="replace")
page_stem = page_path.stem
if page_stem in index_body or str(page_path.relative_to(VAULT_ROOT)) in index_body:
score += INDEX_BOOST
except OSError:
pass
return (score, distinct, total)
def baseline_query(query, top_k=5):
"""Return list of {path, score, distinct, total} for top-K pages."""
terms = tokenize(query)
if not terms:
return []
terms_set = set(terms)
terms_counter = Counter(terms)
scored = []
for p in page_paths():
score, distinct, total = score_page(p, terms_set, terms_counter)
if score > 0:
scored.append({
"path": str(p.relative_to(VAULT_ROOT)),
"score": round(score, 4),
"distinct_terms": distinct,
"total_occurrences": total,
})
scored.sort(key=lambda d: d["score"], reverse=True)
return scored[:top_k]
def main():
parser = argparse.ArgumentParser(description="v1.6 baseline retrieval simulator.")
parser.add_argument("query", help="Natural-language query")
parser.add_argument("--top", type=int, default=5, help="Top-K results")
parser.add_argument("--json", action="store_true", help="Output as JSON")
args = parser.parse_args()
results = baseline_query(args.query, top_k=args.top)
if args.json:
print(json.dumps({
"query": args.query,
"strategy": "baseline-v1.6:hot+index+keyword",
"top_k": args.top,
"candidates": results,
}, indent=2))
else:
if not results:
print("(no matches)")
else:
print(f"v1.6 baseline for: {args.query!r}")
for i, r in enumerate(results, 1):
print(f" {i}. {r['path']} score={r['score']} distinct={r['distinct_terms']} occ={r['total_occurrences']}")
return EXIT_OK
if __name__ == "__main__":
sys.exit(main())
scripts/benchmark-runner.py
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#!/usr/bin/env python3
"""benchmark-runner.py — score v1.7 hybrid retrieval vs v1.6 baseline.
Reads the 50-query corpus at wiki/meta/retrieval-benchmark-v1.7.md, runs both
pipelines for each query, scores top-1 / top-5 accuracy, prints a comparison
table. Used by the v1.7.0 audit.
Pure stdlib + subprocess. No network or LLM calls of its own — the subprocess
calls to retrieve.py may hit ollama (if installed) for rerank. baseline-v16.py
is pure filesystem.
Usage:
benchmark-runner.py # run all 50 queries, print summary
benchmark-runner.py --json results.json # also write per-query results
benchmark-runner.py --limit 5 # smoke: first 5 queries only
"""
import argparse
import json
import re
import subprocess
import sys
from pathlib import Path
VAULT_ROOT = Path(__file__).resolve().parent.parent
CORPUS = VAULT_ROOT / "wiki" / "meta" / "retrieval-benchmark-v1.7.md"
def parse_corpus(corpus_path):
"""Parse the ### <id> blocks into a list of query dicts."""
text = corpus_path.read_text(encoding="utf-8")
# Split on "### " at line start
blocks = re.split(r"\n### ", text)
queries = []
for blk in blocks[1:]: # skip prelude
# First line is the id (e.g. "D1\n")
lines = blk.split("\n", 1)
if len(lines) < 2:
continue
qid = lines[0].strip()
# Ignore non-ID lines (e.g. "Schema", "Scoring rules")
if not re.match(r"^[DH]\d+$", qid):
continue
body = lines[1]
# Stop at next "## " (next section header)
body = re.split(r"\n## ", body, 1)[0]
# Parse fields
def get(field):
m = re.search(rf"^- {field}:\s*(.+)$", body, re.MULTILINE)
return m.group(1).strip() if m else ""
def get_list(field):
raw = get(field)
if not raw or raw == "null":
return []
return [s.strip() for s in raw.split(",") if s.strip()]
queries.append({
"id": qid,
"query": get("query"),
"correct": get_list("correct"),
"relevant": get_list("relevant"),
"category": get("category"),
"rationale": get("rationale"),
})
return queries
def run_v17(query, top_k=5):
"""Returns ordered list of page_paths from v1.7 retrieve.py."""
try:
result = subprocess.run(
["python3", str(VAULT_ROOT / "scripts" / "retrieve.py"),
query, "--top", str(top_k)],
capture_output=True, text=True, timeout=60, check=False,
)
if result.returncode != 0:
return [], f"rc={result.returncode}: {result.stderr.strip()[:200]}"
data = json.loads(result.stdout)
return [c["page_path"] for c in data.get("candidates", [])], None
except (subprocess.TimeoutExpired, json.JSONDecodeError, OSError) as e:
return [], str(e)
def run_v16(query, top_k=5):
"""Returns ordered list of page_paths from v1.6 baseline-v16.py."""
try:
result = subprocess.run(
["python3", str(VAULT_ROOT / "scripts" / "baseline-v16.py"),
query, "--top", str(top_k), "--json"],
capture_output=True, text=True, timeout=30, check=False,
)
if result.returncode != 0:
return [], f"rc={result.returncode}"
data = json.loads(result.stdout)
return [c["path"] for c in data.get("candidates", [])], None
except (subprocess.TimeoutExpired, json.JSONDecodeError, OSError) as e:
return [], str(e)
def score_query(results, correct, relevant, category):
"""Returns (top1_success, top5_success) per the scoring rules."""
# Negative queries: correct is empty; success = no results OR result is in relevant
if category == "negative" or not correct:
if not results:
return (1, 1) # no results = correctly "found nothing"
top1 = 1 if results[0] in relevant else 0
top5 = 1 if any(r in relevant for r in results[:5]) else 0
return (top1, top5)
# Normal queries: top-1 if first result in correct; top-5 if any in correct
top1 = 1 if results and results[0] in correct else 0
top5 = 1 if any(r in correct for r in results[:5]) else 0
return (top1, top5)
def main():
parser = argparse.ArgumentParser()
parser.add_argument("--limit", type=int, default=None, help="Only run first N queries")
parser.add_argument("--json", help="Write per-query results to PATH")
parser.add_argument("--top", type=int, default=5)
args = parser.parse_args()
queries = parse_corpus(CORPUS)
if args.limit:
queries = queries[: args.limit]
print(f"Parsed {len(queries)} queries from {CORPUS.relative_to(VAULT_ROOT)}\n")
per_query = []
cat_stats = {} # category -> {v17_top1, v17_top5, v16_top1, v16_top5, count}
for q in queries:
v17_results, v17_err = run_v17(q["query"], top_k=args.top)
v16_results, v16_err = run_v16(q["query"], top_k=args.top)
v17_top1, v17_top5 = score_query(v17_results, q["correct"], q["relevant"], q["category"])
v16_top1, v16_top5 = score_query(v16_results, q["correct"], q["relevant"], q["category"])
record = {
"id": q["id"],
"category": q["category"],
"query": q["query"][:80] + ("..." if len(q["query"]) > 80 else ""),
"correct": q["correct"],
"v17_top1": v17_top1,
"v17_top5": v17_top5,
"v17_results": v17_results[:args.top],
"v17_err": v17_err,
"v16_top1": v16_top1,
"v16_top5": v16_top5,
"v16_results": v16_results[:args.top],
"v16_err": v16_err,
}
per_query.append(record)
cat = q["category"]
if cat not in cat_stats:
cat_stats[cat] = {"v17_t1": 0, "v17_t5": 0, "v16_t1": 0, "v16_t5": 0, "n": 0}
cat_stats[cat]["v17_t1"] += v17_top1
cat_stats[cat]["v17_t5"] += v17_top5
cat_stats[cat]["v16_t1"] += v16_top1
cat_stats[cat]["v16_t5"] += v16_top5
cat_stats[cat]["n"] += 1
# Live progress
marker = "✓" if v17_top1 else "·"
v16marker = "✓" if v16_top1 else "·"
print(f" {q['id']:4} [{q['category']:14}] v17:{marker} v16:{v16marker} {q['query'][:60]}")
# Aggregate
total_v17_t1 = sum(c["v17_t1"] for c in cat_stats.values())
total_v17_t5 = sum(c["v17_t5"] for c in cat_stats.values())
total_v16_t1 = sum(c["v16_t1"] for c in cat_stats.values())
total_v16_t5 = sum(c["v16_t5"] for c in cat_stats.values())
total_n = sum(c["n"] for c in cat_stats.values())
def pct(x, n):
return f"{100.0 * x / n:5.1f}%" if n else " n/a"
print()
print("=" * 80)
print(f"{'Category':<16} {'N':>4} {'v17 top-1':>10} {'v17 top-5':>10} {'v16 top-1':>10} {'v16 top-5':>10} Δ top-1")
print("-" * 80)
for cat, c in sorted(cat_stats.items()):
delta = (c["v17_t1"] - c["v16_t1"]) / c["n"] * 100 if c["n"] else 0
print(f"{cat:<16} {c['n']:>4} {pct(c['v17_t1'], c['n']):>10} {pct(c['v17_t5'], c['n']):>10} {pct(c['v16_t1'], c['n']):>10} {pct(c['v16_t5'], c['n']):>10} {delta:+6.1f}pp")
delta_total = (total_v17_t1 - total_v16_t1) / total_n * 100 if total_n else 0
print("-" * 80)
print(f"{'TOTAL':<16} {total_n:>4} {pct(total_v17_t1, total_n):>10} {pct(total_v17_t5, total_n):>10} {pct(total_v16_t1, total_n):>10} {pct(total_v16_t5, total_n):>10} {delta_total:+6.1f}pp")
print()
print(f"Plan §7 ship-gate target: ≥30 percentage-point improvement in top-1")
print(f"Actual: {delta_total:+.1f}pp ({'PASS' if delta_total >= 30 else 'INFO'} — pp gain alone, not failure-reduction %)")
# Also compute as a relative reduction in "wrong page cited" errors
v17_wrong = total_n - total_v17_t1
v16_wrong = total_n - total_v16_t1
err_reduction = (v16_wrong - v17_wrong) / v16_wrong * 100 if v16_wrong else 0
print(f"Error-reduction (the gate's actual framing): {err_reduction:+.1f}% ({'PASS' if err_reduction >= 30 else 'FAIL'})")
print()
if args.json:
Path(args.json).write_text(json.dumps({
"summary": {
"v17_top1_pct": 100 * total_v17_t1 / total_n if total_n else 0,
"v17_top5_pct": 100 * total_v17_t5 / total_n if total_n else 0,
"v16_top1_pct": 100 * total_v16_t1 / total_n if total_n else 0,
"v16_top5_pct": 100 * total_v16_t5 / total_n if total_n else 0,
"delta_top1_pp": delta_total,
"error_reduction_pct": err_reduction,
},
"by_category": {cat: {**c, "v17_top1_pct": 100*c["v17_t1"]/c["n"], "v16_top1_pct": 100*c["v16_t1"]/c["n"]} for cat, c in cat_stats.items()},
"per_query": per_query,
}, indent=2, ensure_ascii=False), encoding="utf-8")
print(f"Wrote per-query results to {args.json}")
if __name__ == "__main__":
main()
scripts/bm25-index.py
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#!/usr/bin/env python3
"""bm25-index.py — sparse BM25 inverted index over contextualized wiki chunks.
Pure stdlib (no rank_bm25 dep). Standard Okapi BM25 with k1=1.5, b=0.75.
Indexes the `contextualized_text` field of every chunk under .vault-meta/chunks/,
emits a single JSON file at .vault-meta/bm25/index.json with the schema below.
Concurrency:
- Locks .vault-meta/.bm25.lock (fcntl exclusive) around any index write.
- Atomic .tmp + rename for the index file.
Index schema (.vault-meta/bm25/index.json):
{
"schema_version": 1,
"params": {"k1": 1.5, "b": 0.75},
"doc_count": 1234,
"avg_dl": 487.5,
"updated_at": "2026-05-17T...",
"vocab": {
"<term>": {"df": 17, "postings": [["c-000001:0", 3], ["c-000042:2", 1], ...]}
},
"docs": {
"<chunk_id>": {"path": ".vault-meta/chunks/c-000001/chunk-000.json", "dl": 487}
}
}
Chunk id format: "<page-address>:<chunk-index>" (e.g. "c-000042:3").
Tokenization: lowercase, collapse whitespace, drop punctuation except in-word
apostrophes and hyphens. ASCII-only stopwords filtered (small list; favors
recall over precision).
Query interface (used by retrieve.py at query time):
bm25-index.py query "your text here" [--top 20]
Build interface:
bm25-index.py build # full rebuild (always; incremental is v1.7.x scope)
bm25-index.py stats # print index stats
Exit codes:
0 — success
1 — lock acquisition failed
2 — usage error
3 — index file missing or corrupt (query mode)
4 — chunks directory missing
"""
import argparse
import fcntl
import json
import math
import os
import re
import sys
from collections import Counter, defaultdict
from datetime import datetime, timezone
from pathlib import Path
VAULT_ROOT = Path(__file__).resolve().parent.parent
META_DIR = VAULT_ROOT / ".vault-meta"
CHUNKS_DIR = META_DIR / "chunks"
BM25_DIR = META_DIR / "bm25"
INDEX_PATH = BM25_DIR / "index.json"
LOCK_PATH = META_DIR / ".bm25.lock"
K1 = 1.5
B = 0.75
# Small high-frequency-stopword list (English). Conservative — keep recall high.
STOPWORDS = frozenset("""
a an and are as at be by for from has have he her him his i if in is it its
of on or that the their them they this to was were will with you your
""".split())
# Unicode-aware tokenizer (v1.7.2; closes audit M2). \w under re.UNICODE
# matches letters and digits from any script (CJK, Cyrillic, accented Latin,
# Devanagari, etc.) plus underscore. Internal apostrophes and hyphens are
# preserved so "user's" and "well-formed" stay single tokens. Pure-symbol or
# pure-emoji tokens fail the leading \w anchor and are correctly skipped.
TOKEN_RE = re.compile(r"\w[\w'\-]*", re.UNICODE)
EXIT_OK = 0
EXIT_LOCK = 1
EXIT_USAGE = 2
EXIT_INDEX_MISSING = 3
EXIT_NO_CHUNKS = 4
def log(msg):
print(msg, file=sys.stderr)
def tokenize(text):
"""Lowercase, strip punctuation, drop stopwords. Returns a list of terms."""
return [t.lower() for t in TOKEN_RE.findall(text)
if t.lower() not in STOPWORDS and len(t) > 1]
def acquire_lock():
META_DIR.mkdir(parents=True, exist_ok=True)
fd = os.open(str(LOCK_PATH), os.O_CREAT | os.O_WRONLY, 0o644)
try:
fcntl.flock(fd, fcntl.LOCK_EX | fcntl.LOCK_NB)
except OSError:
os.close(fd)
log("ERR: could not acquire bm25 lock")
sys.exit(EXIT_LOCK)
return fd
def release_lock(fd):
try:
fcntl.flock(fd, fcntl.LOCK_UN)
finally:
os.close(fd)
def discover_chunks():
"""Yield (chunk_id, path, contextualized_text) for every chunk on disk.
The yielded `path` is relative to the directory two levels above CHUNKS_DIR
(i.e. .vault-meta/chunks/<addr>/ → relative to the vault root). This works
both in production (CHUNKS_DIR is `<vault>/.vault-meta/chunks`) and when
tests monkey-patch CHUNKS_DIR to a sandbox `<tmp>/.vault-meta/chunks`.
"""
if not CHUNKS_DIR.is_dir():
log(f"ERR: no chunks directory at {CHUNKS_DIR}")
sys.exit(EXIT_NO_CHUNKS)
rel_root = CHUNKS_DIR.parent.parent
for chunk_file in sorted(CHUNKS_DIR.glob("*/chunk-*.json")):
try:
data = json.loads(chunk_file.read_text(encoding="utf-8"))
except (json.JSONDecodeError, OSError) as e:
log(f" skip (unreadable): {chunk_file} — {e}")
continue
address = data.get("page_address")
idx = data.get("chunk_index")
text = data.get("contextualized_text") or data.get("raw_text", "")
if address is None or idx is None:
continue
chunk_id = f"{address}:{idx}"
rel_path = str(chunk_file.relative_to(rel_root))
yield chunk_id, rel_path, text
def build_index():
docs = {}
df = Counter()
postings = defaultdict(list)
for chunk_id, rel_path, text in discover_chunks():
tokens = tokenize(text)
tf = Counter(tokens)
docs[chunk_id] = {"path": rel_path, "dl": len(tokens)}
for term, count in tf.items():
df[term] += 1
postings[term].append([chunk_id, count])
if not docs:
log("WARN: no chunks indexed")
return None
avg_dl = sum(d["dl"] for d in docs.values()) / len(docs)
vocab = {term: {"df": df[term], "postings": postings[term]}
for term in sorted(df.keys())}
return {
"schema_version": 1,
"params": {"k1": K1, "b": B},
"doc_count": len(docs),
"avg_dl": avg_dl,
"updated_at": datetime.now(timezone.utc).strftime("%Y-%m-%dT%H:%M:%SZ"),
"vocab": vocab,
"docs": docs,
}
def write_index(index):
BM25_DIR.mkdir(parents=True, exist_ok=True)
tmp = INDEX_PATH.with_suffix(f".{os.getpid()}.tmp")
try:
tmp.write_text(json.dumps(index, ensure_ascii=False), encoding="utf-8")
os.replace(tmp, INDEX_PATH)
finally:
if tmp.exists():
tmp.unlink(missing_ok=True)
def load_index():
if not INDEX_PATH.is_file():
log(f"ERR: no index at {INDEX_PATH}. Run `bm25-index.py build` first.")
sys.exit(EXIT_INDEX_MISSING)
try:
return json.loads(INDEX_PATH.read_text(encoding="utf-8"))
except (json.JSONDecodeError, OSError) as e:
log(f"ERR: index corrupt: {e}")
sys.exit(EXIT_INDEX_MISSING)
def query(text, top_k=20):
idx = load_index()
vocab = idx["vocab"]
docs = idx["docs"]
params = idx["params"]
avg_dl = idx["avg_dl"]
N = idx["doc_count"]
k1 = params["k1"]
b = params["b"]
qterms = tokenize(text)
if not qterms:
return []
# Defensive guard (v1.7.2; closes audit L7): avg_dl can only be 0 if the
# vocab is also empty (all chunks have zero tokens), in which case the
# loop never enters this divide path. But future refactors could change
# that invariant; the `or 1.0` keeps it safe by construction.
avg_dl_safe = avg_dl or 1.0
scores = defaultdict(float)
for term in qterms:
v = vocab.get(term)
if not v:
continue
df = v["df"]
idf = math.log(1 + (N - df + 0.5) / (df + 0.5))
for cid, cnt in v["postings"]:
dl = docs[cid]["dl"]
denom = cnt + k1 * (1 - b + b * dl / avg_dl_safe)
scores[cid] += idf * (cnt * (k1 + 1)) / denom
ranked = sorted(scores.items(), key=lambda kv: kv[1], reverse=True)[:top_k]
return [
{
"chunk_id": cid,
"score": round(score, 6),
"path": docs[cid]["path"],
}
for cid, score in ranked
]
def stats():
idx = load_index()
print(json.dumps({
"doc_count": idx["doc_count"],
"avg_dl": round(idx["avg_dl"], 2),
"vocab_size": len(idx["vocab"]),
"updated_at": idx["updated_at"],
"params": idx["params"],
}, indent=2))
def main():
parser = argparse.ArgumentParser(description="BM25 inverted index over wiki chunks.")
sub = parser.add_subparsers(dest="cmd", required=True)
sub.add_parser("build", help="Build the index (full rebuild every time in v1.7).")
sp_query = sub.add_parser("query", help="Query the index.")
sp_query.add_argument("text", help="Query text")
sp_query.add_argument("--top", type=int, default=20, help="Top-K results")
sub.add_parser("stats", help="Print index stats.")
args = parser.parse_args()
if args.cmd == "build":
fd = acquire_lock()
try:
index = build_index()
if index is None:
log("Nothing to index.")
return EXIT_OK
write_index(index)
log(f"Wrote {INDEX_PATH} docs={index['doc_count']} vocab={len(index['vocab'])} avg_dl={index['avg_dl']:.1f}")
finally:
release_lock(fd)
return EXIT_OK
if args.cmd == "query":
results = query(args.text, top_k=args.top)
print(json.dumps(results, indent=2))
return EXIT_OK
if args.cmd == "stats":
stats()
return EXIT_OK
return EXIT_USAGE
if __name__ == "__main__":
sys.exit(main())
scripts/boundary-score.py
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#!/usr/bin/env python3
"""boundary-score.py — DragonScale Mechanism 4: boundary-first autoresearch scorer.
Reads `wiki/**/*.md`, builds a wikilink graph, and emits per-page boundary
scores to stdout (text) or as JSON for tooling.
boundary_score(p) = (out_degree(p) - in_degree(p)) * recency_weight(p)
- out_degree(p): count of distinct wikilinks in p that resolve to a
scoreable page (scoreable = non-meta, non-fold, non-excluded).
- in_degree(p): count of distinct scoreable pages that link to p.
- recency_weight(p): exp(-days_since_updated / RECENCY_HALFLIFE_DAYS).
No floor; very old pages approach zero weight, which is the intended
semantic of "frontier" (recently-touched and outward-pointing).
High score = the page points at many things, is pointed at by few, and
has been touched recently. That is a vault frontier page. Low or
negative score = hub / integrated page.
Feature-gated opt-in: autoresearch only invokes this when DragonScale
setup is detected. Safe to run standalone even without DragonScale set
up (reads wiki/ only; never writes).
This script is intentionally stdout-only. There is no `--report PATH`
equivalent to `tiling-check.py --report` because the helper is small
enough to pipe directly (`./scripts/boundary-score.py --json | jq ...`)
and keeping it read-only removes a write-path attack surface.
Usage:
boundary-score.py # top-10 frontier, text
boundary-score.py --top N # top N frontier
boundary-score.py --json # JSON output
boundary-score.py --page PATH # score for a single page
boundary-score.py --include-score-zero # include pages with score=0
Exit codes:
0 success
2 usage error
"""
import argparse
import json
import math
import re
import sys
from datetime import date, datetime, timezone
from pathlib import Path
VAULT_ROOT = Path(__file__).resolve().parent.parent
WIKI_DIR = VAULT_ROOT / "wiki"
EXCLUDE_TYPES = {"meta", "fold"}
EXCLUDE_FILENAMES = {
"_index.md", "index.md", "log.md", "hot.md", "overview.md",
"dashboard.md", "Wiki Map.md", "getting-started.md",
}
EXCLUDE_PATH_PREFIXES = ("wiki/folds/", "wiki/meta/")
RECENCY_HALFLIFE_DAYS = 30.0
# No recency floor: a truly stale page should NOT dominate the frontier
# ranking, even if its out-degree is high. The exponential decay takes
# weight toward zero for year-old pages, which is the intended semantic
# of "frontier" (recently-touched and outward-pointing).
DEFAULT_TOP = 10
MAX_BODY_BYTES = 256 * 1024
# CommonMark-ish fence tracking: opening fence records (char, length);
# a closing fence must use the SAME char with SAME-OR-LONGER run length.
# Tilde fences (~~~) are supported alongside backtick fences (```). Indented
# code blocks (4+ spaces) are NOT filtered; in Obsidian usage, indented
# bullets commonly contain wikilinks and should count as edges.
FRONTMATTER_RE = re.compile(r"^---\n(.*?)\n---\n", re.DOTALL)
TYPE_RE = re.compile(r"^type:\s*(\S+)", re.MULTILINE)
UPDATED_RE = re.compile(r"^updated:\s*([0-9]{4}-[0-9]{2}-[0-9]{2})", re.MULTILINE)
CREATED_RE = re.compile(r"^created:\s*([0-9]{4}-[0-9]{2}-[0-9]{2})", re.MULTILINE)
TITLE_RE = re.compile(r'^title:\s*"?([^"\n]+?)"?\s*$', re.MULTILINE)
# Obsidian wikilinks: [[Target]] or [[Target|Alias]] or [[Target#Heading]]
WIKILINK_RE = re.compile(r"\[\[([^\]|#]+)(?:#[^\]|]+)?(?:\|[^\]]+)?\]\]")
EXIT_OK = 0
EXIT_USAGE = 2
def log(msg: str) -> None:
print(msg, file=sys.stderr)
def parse_frontmatter(text: str) -> tuple[dict, str]:
m = FRONTMATTER_RE.match(text)
if not m:
return {}, text
fm_raw = m.group(1)
body = text[m.end():]
fm: dict = {}
for key, regex in (("type", TYPE_RE), ("updated", UPDATED_RE),
("created", CREATED_RE), ("title", TITLE_RE)):
tm = regex.search(fm_raw)
if tm:
fm[key] = tm.group(1).strip().strip('"').strip("'")
return fm, body
def included(path: Path, fm: dict) -> bool:
if path.is_symlink():
return False
try:
resolved = path.resolve(strict=True)
resolved.relative_to(VAULT_ROOT.resolve())
except (OSError, ValueError):
return False
rel = path.relative_to(VAULT_ROOT).as_posix()
if path.name in EXCLUDE_FILENAMES:
return False
for prefix in EXCLUDE_PATH_PREFIXES:
if rel.startswith(prefix):
return False
if fm.get("type") in EXCLUDE_TYPES:
return False
return True
def days_since(date_str: str | None) -> float:
"""Return days since the given YYYY-MM-DD string, or a large sentinel if missing."""
if not date_str:
return 10_000.0
try:
d = date.fromisoformat(date_str)
except ValueError:
return 10_000.0
delta = (date.today() - d).days
return max(0.0, float(delta))
def recency_weight(days: float,
halflife: float = RECENCY_HALFLIFE_DAYS) -> float:
return math.exp(-days / halflife)
_FENCE_RE = re.compile(r"^(\s*)(`{3,}|~{3,})")
def extract_wikilinks(body: str) -> set[str]:
"""Extract unique link targets (without alias or heading suffix) from the body.
Skips wikilinks inside fenced code blocks so documentation examples
(including in this repo's own skill files) do not pollute the graph.
Fence handling: backtick AND tilde fences, with length tracking per
CommonMark: the opening run sets (char, min_len); the closing line
must use the SAME char with a run of SAME-OR-LONGER length. Indented
code blocks (4+ spaces) are intentionally NOT filtered — indented
bullets in Obsidian often contain wikilinks.
"""
cleaned: list[str] = []
fence_char: str | None = None
fence_len: int = 0
for line in body.splitlines():
m = _FENCE_RE.match(line)
if m:
char = m.group(2)[0]
length = len(m.group(2))
if fence_char is None:
fence_char = char
fence_len = length
continue
if char == fence_char and length >= fence_len:
fence_char = None
fence_len = 0
continue
if fence_char is not None:
continue
cleaned.append(line)
scan = "\n".join(cleaned)
results: set[str] = set()
for m in WIKILINK_RE.finditer(scan):
raw = m.group(1).strip()
# Folder-qualified links like [[notes/Foo]] resolve to Foo.md by stem.
# This matches Obsidian default behavior for unique filenames.
stem = raw.rsplit("/", 1)[-1]
if stem:
results.add(stem)
return results
def collect_pages() -> dict[str, dict]:
"""Scan wiki/, return {title_key: {path, title, body, fm}} for scoreable pages.
`title_key` is the filename stem, which is what Obsidian wikilinks resolve
to by default. Assumes filenames are unique across the vault (enforced by
wiki-lint naming convention).
"""
pages: dict[str, dict] = {}
if not WIKI_DIR.is_dir():
return pages
for md in sorted(WIKI_DIR.rglob("*.md")):
try:
text = md.read_text(encoding="utf-8")
except (OSError, UnicodeDecodeError):
continue
if len(text.encode("utf-8")) > MAX_BODY_BYTES:
continue
fm, body = parse_frontmatter(text)
if not included(md, fm):
continue
title_key = md.stem # Obsidian wikilinks are filename-based
pages[title_key] = {
"path": md.relative_to(VAULT_ROOT).as_posix(),
"title": fm.get("title", title_key),
"body": body,
"fm": fm,
}
return pages
def build_graph(pages: dict[str, dict]) -> tuple[dict[str, set[str]], dict[str, set[str]]]:
"""Return (out_edges, in_edges) where each maps title_key -> set(title_key).
Only edges whose target is a known scoreable page are counted. Self-loops
are ignored.
"""
out_edges: dict[str, set[str]] = {k: set() for k in pages}
in_edges: dict[str, set[str]] = {k: set() for k in pages}
for src, entry in pages.items():
links = extract_wikilinks(entry["body"])
for target in links:
if target == src:
continue
if target in pages:
out_edges[src].add(target)
in_edges[target].add(src)
return out_edges, in_edges
def score_page(title_key: str,
pages: dict[str, dict],
out_edges: dict[str, set[str]],
in_edges: dict[str, set[str]]) -> dict:
entry = pages[title_key]
fm = entry["fm"]
out_deg = len(out_edges.get(title_key, set()))
in_deg = len(in_edges.get(title_key, set()))
date_str = fm.get("updated") or fm.get("created")
days = days_since(date_str)
rw = recency_weight(days)
score = (out_deg - in_deg) * rw
return {
"title": entry["title"],
"title_key": title_key,
"path": entry["path"],
"out_degree": out_deg,
"in_degree": in_deg,
"age_days": days,
"recency_weight": round(rw, 4),
"score": round(score, 4),
}
def run(top: int, want_json: bool, include_zero: bool, page_filter: str | None) -> int:
pages = collect_pages()
out_edges, in_edges = build_graph(pages)
scored = [score_page(k, pages, out_edges, in_edges) for k in pages]
if page_filter:
key = Path(page_filter).stem
matched = [s for s in scored if s["title_key"] == key or s["path"] == page_filter]
if not matched:
log(f"ERR: no scoreable page matches '{page_filter}'")
return EXIT_USAGE
scored = matched
else:
if not include_zero:
scored = [s for s in scored if s["score"] > 0.0]
scored.sort(key=lambda s: (-s["score"], s["title_key"]))
scored = scored[:top]
if want_json:
print(json.dumps({
"generated": datetime.now(timezone.utc).isoformat(timespec="seconds").replace("+00:00", "Z"),
"halflife_days": RECENCY_HALFLIFE_DAYS,
"page_count_scoreable": len(pages),
"results": scored,
}, indent=2))
else:
print("# Boundary Score Report")
print(f"scoreable pages: {len(pages)}; halflife: {RECENCY_HALFLIFE_DAYS} days")
if not scored:
print("\nNo positive-score frontier pages found.")
else:
print("")
print("| # | score | out | in | age_d | title | path |")
print("|---|---|---|---|---|---|---|")
for i, s in enumerate(scored, 1):
print(f"| {i} | {s['score']:.3f} | {s['out_degree']} | {s['in_degree']} | "
f"{int(s['age_days'])} | {s['title']} | {s['path']} |")
return EXIT_OK
def main(argv: list[str]) -> int:
p = argparse.ArgumentParser()
p.add_argument("--top", type=int, default=DEFAULT_TOP)
p.add_argument("--json", action="store_true")
p.add_argument("--include-score-zero", action="store_true",
help="Include pages whose score is zero or negative in the output")
p.add_argument("--page", default=None, help="Score a single page by path or stem")
args = p.parse_args(argv)
if args.top < 1:
log("ERR: --top must be >= 1")
return EXIT_USAGE
return run(args.top, args.json, args.include_score_zero, args.page)
if __name__ == "__main__":
sys.exit(main(sys.argv[1:]))
scripts/contextual-prefix.py
+505
View File
@@ -0,0 +1,505 @@
#!/usr/bin/env python3
"""contextual-prefix.py — chunk wiki pages and generate per-chunk contextual prefixes.
Implements the ingest-side of Anthropic's Sept 2024 Contextual Retrieval pattern
(https://www.anthropic.com/news/contextual-retrieval). For each chunk of a wiki
page, generates a 1-2 sentence prefix situating the chunk in its source. The
prefixed text is what gets BM25-indexed and embedded, materially improving
retrieval accuracy (Anthropic measured 35-49% failure reduction).
Three-tier prefix generation (chosen per-run automatically):
1. If ANTHROPIC_API_KEY is set → direct Anthropic API call (Haiku 4.5)
with prompt caching on the page body
(only when the body clears the ~16 KB
Haiku 4.5 cache floor; see
cache_control_for()).
~$12 / 1000 docs per Anthropic figures.
REQUIRES --allow-egress (sends bodies off-machine).
2. Elif `claude` binary on PATH → `claude -p` subprocess (uses CC subscription;
no API key needed; slower per call).
REQUIRES --allow-egress (subprocess egresses).
3. Else (default) → synthetic prefix from page frontmatter +
first paragraph (zero-cost floor; loses
most of the contextual benefit but BM25
and vector channels still work).
Data-egress posture (v1.7.1+):
Tiers 1 and 2 send wiki page bodies off-machine. Both are GATED behind
--allow-egress (default off). Without the flag, pick_prefix_tier() always
returns "synthetic" regardless of env vars or claude binary presence.
Mirror of scripts/tiling-check.py:351 --allow-remote-ollama precedent.
Chunk schema written to .vault-meta/chunks/<page-address>/chunk-NNN.json:
{
"schema_version": 1,
"page_path": "wiki/concepts/Foo.md",
"page_address": "c-000042",
"chunk_index": 3,
"raw_text": "...",
"contextualized_text": "<prefix> <raw_text>",
"prefix_source": "anthropic-api" | "claude-cli" | "synthetic" | "skipped",
"char_count": 487,
"body_hash": "sha256:...", # of raw_text
"page_body_hash": "sha256:...", # of the WHOLE source page (for invalidation)
"created_at": "2026-05-17T..."
}
Pages without an `address:` frontmatter field are still chunked (using a
synthetic address derived from the path slug) so this tool works on v1.6 vaults
without DragonScale Mechanism 2 enabled.
Usage:
contextual-prefix.py PATH # process a single page
contextual-prefix.py --all # process every wiki/*.md
contextual-prefix.py PATH --no-llm # force synthetic-prefix tier 3
contextual-prefix.py PATH --rebuild # ignore existing chunks
contextual-prefix.py PATH --peek # print what would happen; write nothing
Exit codes:
0 — success
2 — usage error
3 — page file missing or unreadable
4 — chunk dir creation failed
"""
import argparse
import hashlib
import json
import os
import re
import shutil
import subprocess
import sys
import urllib.error
import urllib.request
from datetime import datetime, timezone
from pathlib import Path
VAULT_ROOT = Path(__file__).resolve().parent.parent
WIKI_DIR = VAULT_ROOT / "wiki"
META_DIR = VAULT_ROOT / ".vault-meta"
CHUNKS_DIR = META_DIR / "chunks"
CHUNK_TARGET_TOKENS = 500 # rough; we approximate via chars/4
CHUNK_TARGET_CHARS = CHUNK_TARGET_TOKENS * 4
CHUNK_OVERLAP_CHARS = 200
ANTHROPIC_MODEL = "claude-haiku-4-5-20251001"
ANTHROPIC_API_URL = "https://api.anthropic.com/v1/messages"
ANTHROPIC_TIMEOUT_SEC = 30
CLAUDE_CLI_TIMEOUT_SEC = 60
# Anthropic prompt caching ignores any cached prefix below the model's minimum
# cacheable size — 4,096 tokens for Haiku 4.5 (verified against the prompt-caching
# docs, 2026-05). At ~4 chars/token that is ~16 KB. We attach cache_control only
# when the body clears this floor so the marker reflects reality: below the floor
# the API treats it as a silent no-op. The per-call cache telemetry in
# anthropic_api_prefix() is what actually measures hit rate. The check counts the
# body only — a deliberately conservative ~370-char underestimate that ignores the
# system_msg + <page> wrapper also inside the cached prefix — so near the boundary
# it errs toward not-marking, never toward a wrongly-attached marker.
HAIKU_CACHE_MIN_CHARS = 16384 # 4096 tokens * 4 chars/token
EXIT_OK = 0
EXIT_USAGE = 2
EXIT_PAGE_MISSING = 3
EXIT_CHUNK_DIR = 4
FRONTMATTER_RE = re.compile(r"^---\n(.*?)\n---\n", re.DOTALL)
ADDRESS_RE = re.compile(r"^address:\s*(c-\d{6})\s*$", re.MULTILINE)
TITLE_RE = re.compile(r"^title:\s*['\"]?(.+?)['\"]?\s*$", re.MULTILINE)
def log(msg):
print(msg, file=sys.stderr)
def sha256(text):
return "sha256:" + hashlib.sha256(text.encode("utf-8")).hexdigest()
def read_page(path):
if not path.is_file():
raise SystemExit(EXIT_PAGE_MISSING)
return path.read_text(encoding="utf-8", errors="replace")
def parse_frontmatter(body):
m = FRONTMATTER_RE.match(body)
if not m:
return {}, body
fm_text = m.group(1)
rest = body[m.end():]
addr_m = ADDRESS_RE.search(fm_text)
title_m = TITLE_RE.search(fm_text)
return {
"address": addr_m.group(1) if addr_m else None,
"title": title_m.group(1) if title_m else None,
"raw": fm_text,
}, rest
def derive_synthetic_address(page_path):
"""Stable per-path address-shaped string when no real address is set.
Format: c-NNNNNN derived from a hash of the relative path (deterministic).
Distinct from allocator addresses; used only for chunk filing.
"""
rel = page_path.relative_to(VAULT_ROOT)
h = hashlib.sha1(str(rel).encode("utf-8")).hexdigest()
return "syn-" + h[:6]
def chunk_body(body, target_chars=CHUNK_TARGET_CHARS, overlap=CHUNK_OVERLAP_CHARS):
"""Split body into overlapping chunks on paragraph boundaries when possible.
Heuristic: walk the body, accumulate paragraphs until len exceeds target,
flush, then keep the trailing `overlap` chars as the seed of the next chunk.
Empty paragraphs collapse to single boundaries.
"""
paragraphs = [p.strip() for p in re.split(r"\n\s*\n", body) if p.strip()]
chunks = []
cur = []
cur_len = 0
for p in paragraphs:
cur.append(p)
cur_len += len(p) + 2
if cur_len >= target_chars:
chunk_text = "\n\n".join(cur)
chunks.append(chunk_text)
# seed next chunk with the tail
tail = chunk_text[-overlap:] if overlap > 0 else ""
cur = [tail] if tail else []
cur_len = len(tail)
if cur and "".join(cur).strip():
chunks.append("\n\n".join(cur))
if not chunks and body.strip():
# tiny page — single chunk
chunks = [body.strip()]
return chunks
def synthetic_prefix(fm, body, chunk_text):
"""Tier-3 prefix: page title + first sentence of the page body.
Free, hermetic, deterministic. Provides modest BM25 lift via title-word
re-injection into the chunk corpus.
"""
title = (fm.get("title") or "").strip() or "(untitled)"
# First sentence of the body (not the chunk — gives the chunk a page-level frame)
first_sentence = re.split(r"(?<=[.!?])\s+", body.strip(), maxsplit=1)
first = first_sentence[0][:300] if first_sentence else ""
return f"This passage is from the wiki page \"{title}\". The page opens: {first}"
def cache_control_for(page_body):
"""Ephemeral cache_control dict when the page body clears the Haiku cache
floor, else None. Pure function so the floor decision is unit-testable
without the network (the API call itself stays egress-gated).
"""
if len(page_body) >= HAIKU_CACHE_MIN_CHARS:
return {"type": "ephemeral"}
return None
def anthropic_api_prefix(api_key, page_title, page_body, chunk_text):
"""Tier-1 prefix: direct Anthropic API call, Haiku, prompt-cached page body.
The page body is the stable prefix shared by every chunk of a page, so it
goes in `system` behind a cache breakpoint and the variable chunk goes in
`messages`. Cache reads only land because chunks are processed sequentially
(chunk 0 warms the prefix) — see the loop note in process_page().
"""
system_msg = (
"You are a retrieval-augmentation assistant. Given a wiki page and one "
"chunk extracted from it, write a single short sentence (under 35 words) "
"that situates the chunk within the page's scope and topic. Output only "
"the sentence — no prefix, no quotation marks, no commentary."
)
page_block = {
"type": "text",
"text": f"<page title=\"{page_title}\">\n{page_body}\n</page>",
}
cc = cache_control_for(page_body)
if cc:
page_block["cache_control"] = cc
payload = {
"model": ANTHROPIC_MODEL,
"max_tokens": 100,
"system": [
{"type": "text", "text": system_msg},
page_block,
],
"messages": [
{
"role": "user",
"content": (
"Write the single contextualizing sentence for this chunk:\n\n"
f"<chunk>\n{chunk_text}\n</chunk>"
),
}
],
}
body = json.dumps(payload).encode("utf-8")
req = urllib.request.Request(
ANTHROPIC_API_URL,
data=body,
headers={
"Content-Type": "application/json",
"x-api-key": api_key,
"anthropic-version": "2023-06-01",
},
method="POST",
)
try:
with urllib.request.urlopen(req, timeout=ANTHROPIC_TIMEOUT_SEC) as resp:
data = json.loads(resp.read().decode("utf-8"))
# Cache telemetry: integer token counts only, never page content, so
# the data-egress posture holds. Confirms whether the body cache is
# actually firing given the Haiku floor (wrote>0 on chunk 0, read>0
# on later chunks of the same page).
usage = data.get("usage", {})
log(f" cache: wrote={usage.get('cache_creation_input_tokens', 0)} "
f"read={usage.get('cache_read_input_tokens', 0)} tok")
for block in data.get("content", []):
if block.get("type") == "text":
return block["text"].strip().splitlines()[0]
except (urllib.error.URLError, json.JSONDecodeError, KeyError) as e:
log(f" anthropic-api call failed: {e}")
return None
return None
def claude_cli_prefix(page_title, page_body, chunk_text):
"""Tier-2 prefix: `claude -p` subprocess (uses CC subscription, no API key)."""
prompt = (
f"Wiki page \"{page_title}\":\n\n"
f"---\n{page_body[:4000]}\n---\n\n"
f"Chunk:\n<chunk>\n{chunk_text}\n</chunk>\n\n"
"Write one short sentence (under 35 words) situating this chunk within "
"the page's scope. Output only the sentence."
)
try:
result = subprocess.run(
["claude", "-p", prompt],
capture_output=True,
text=True,
timeout=CLAUDE_CLI_TIMEOUT_SEC,
check=False,
)
if result.returncode == 0 and result.stdout.strip():
return result.stdout.strip().splitlines()[0]
log(f" claude-cli rc={result.returncode}: {result.stderr.strip()[:200]}")
except (subprocess.TimeoutExpired, FileNotFoundError) as e:
log(f" claude-cli call failed: {e}")
return None
def pick_prefix_tier(force_synthetic, allow_egress=False):
"""Choose the contextual-prefix generation tier.
Without allow_egress=True, ALWAYS returns "synthetic" regardless of
env vars or claude binary availability. This is the v1.7.1 data-egress
guard: tiers 1 (Anthropic API) and 2 (claude CLI subprocess) both send
wiki page bodies off-machine, so they require explicit user consent via
the --allow-egress flag at the CLI layer.
Mirrors scripts/tiling-check.py:351 --allow-remote-ollama default-deny.
"""
if force_synthetic or not allow_egress:
return "synthetic"
if os.environ.get("ANTHROPIC_API_KEY"):
return "anthropic-api"
if shutil.which("claude"):
return "claude-cli"
return "synthetic"
def generate_prefix(tier, fm, body, chunk_text):
"""Asymmetric fallback by design:
- tier="anthropic-api" → on failure, try claude-cli (subprocess,
free) before synthetic. The API is the user's stated preference,
and claude-cli is the closer-in-quality fallback.
- tier="claude-cli" → on failure, go straight to synthetic. The
user has either no API key or has not opted into one; climbing
back to the API would silently spend money they did not authorize.
- tier="synthetic" → always synthetic.
"""
title = fm.get("title") or "(untitled)"
if tier == "anthropic-api":
result = anthropic_api_prefix(
os.environ["ANTHROPIC_API_KEY"], title, body, chunk_text
)
if result:
return result, "anthropic-api"
if shutil.which("claude"):
result = claude_cli_prefix(title, body, chunk_text)
if result:
return result, "claude-cli"
return synthetic_prefix(fm, body, chunk_text), "synthetic"
if tier == "claude-cli":
result = claude_cli_prefix(title, body, chunk_text)
if result:
return result, "claude-cli"
return synthetic_prefix(fm, body, chunk_text), "synthetic"
return synthetic_prefix(fm, body, chunk_text), "synthetic"
def process_page(page_path, force_synthetic=False, rebuild=False, peek=False,
allow_egress=False, progress_label=""):
body = read_page(page_path)
fm, content = parse_frontmatter(body)
address = fm.get("address") or derive_synthetic_address(page_path)
page_body_hash = sha256(body)
chunk_dir = CHUNKS_DIR / address
if not peek:
try:
chunk_dir.mkdir(parents=True, exist_ok=True)
except OSError as e:
log(f"ERR: cannot create chunk dir {chunk_dir}: {e}")
raise SystemExit(EXIT_CHUNK_DIR)
chunks = chunk_body(content)
tier = pick_prefix_tier(force_synthetic, allow_egress=allow_egress)
progress = (progress_label + " ") if progress_label else ""
if not chunks:
# v1.7.2 / closes audit M6: previously this logged "chunks=0" with no
# explanation and silently produced no index entries. Now: explicit WARN
# so the user notices empty-body pages (often frontmatter-only stubs).
log(f"{progress}WARN: {page_path.relative_to(VAULT_ROOT)} has no chunkable body content "
f"(empty after frontmatter strip). Skipping; no chunks written.")
return {"address": address, "written": [], "skipped": 0, "tier": tier}
log(f"{progress}-> {page_path.relative_to(VAULT_ROOT)} address={address} chunks={len(chunks)} tier={tier}")
written = []
skipped = 0
# Keep this loop sequential. The tier-1 Anthropic path caches the page body;
# a cache entry is only readable after the first response begins (Anthropic
# prompt-caching concurrency rule), so chunk 0 warms the prefix and chunks
# 1..N read it. Parallelizing here would silently zero every cache read.
for idx, raw in enumerate(chunks):
chunk_path = chunk_dir / f"chunk-{idx:03d}.json"
body_hash = sha256(raw)
if chunk_path.exists() and not rebuild:
try:
existing = json.loads(chunk_path.read_text(encoding="utf-8"))
if existing.get("body_hash") == body_hash and \
existing.get("page_body_hash") == page_body_hash:
skipped += 1
continue
except (json.JSONDecodeError, OSError):
pass # corrupted; overwrite
if peek:
log(f" would write {chunk_path.name} ({len(raw)} chars)")
continue
prefix, prefix_source = generate_prefix(tier, fm, content, raw)
contextualized = f"{prefix}\n\n{raw}" if prefix else raw
record = {
"schema_version": 1,
"page_path": str(page_path.relative_to(VAULT_ROOT)),
"page_address": address,
"chunk_index": idx,
"raw_text": raw,
"contextualized_text": contextualized,
"prefix": prefix or "",
"prefix_source": prefix_source,
"char_count": len(raw),
"body_hash": body_hash,
"page_body_hash": page_body_hash,
"created_at": datetime.now(timezone.utc).strftime("%Y-%m-%dT%H:%M:%SZ"),
}
tmp = chunk_path.with_suffix(f".{os.getpid()}.tmp")
try:
tmp.write_text(json.dumps(record, ensure_ascii=False, indent=2), encoding="utf-8")
os.replace(tmp, chunk_path)
finally:
if tmp.exists():
tmp.unlink(missing_ok=True)
written.append(chunk_path.name)
log(f" wrote={len(written)} skipped(unchanged)={skipped}")
return {"address": address, "written": written, "skipped": skipped, "tier": tier}
def collect_pages(target):
if target == "--all" or target is None:
return sorted(p for p in WIKI_DIR.rglob("*.md")
if not any(part.startswith(".") for part in p.parts))
p = Path(target)
if not p.is_absolute():
p = VAULT_ROOT / p
return [p]
def main():
parser = argparse.ArgumentParser(description="Chunk + contextualize wiki pages.")
parser.add_argument("path", nargs="?",
help="Page path relative to vault root. Omit (or pass --all) "
"to process every wiki page.")
parser.add_argument("--all", action="store_true",
help="Process every wiki page (equivalent to omitting path).")
parser.add_argument("--no-llm", action="store_true",
help="Force tier-3 synthetic prefix (skip LLM calls).")
parser.add_argument("--allow-egress", action="store_true",
help="Allow tier-1 (Anthropic API) or tier-2 (claude CLI "
"subprocess) prefix generation. Without this flag, page "
"bodies stay on-machine and only the tier-3 synthetic "
"prefix is used. Mirror of tiling-check.py's "
"--allow-remote-ollama guard.")
parser.add_argument("--rebuild", action="store_true",
help="Re-process chunks even if body_hash matches.")
parser.add_argument("--peek", action="store_true",
help="Print plan, write nothing.")
args = parser.parse_args()
if args.all and not args.path:
args.path = "--all"
elif not args.path:
# No path and no --all: default to all (matches the help text)
args.path = "--all"
pages = collect_pages(args.path)
# Explicit single-path invocations must point at a readable file inside the
# vault. --all only ever yields in-vault files, so this guard is explicit-only.
# Without it a typo'd path exited 0 silently, and an out-of-vault path raised
# a raw ValueError from relative_to().
if args.path != "--all":
target = pages[0].resolve()
if not target.is_relative_to(VAULT_ROOT):
log(f"ERR: {args.path} resolves outside the vault ({VAULT_ROOT}).")
return EXIT_USAGE
if not target.is_file():
log(f"ERR: {args.path} is not a readable file.")
return EXIT_PAGE_MISSING
# Filter to actual files up front so progress counter is meaningful
# (v1.7.2; closes audit L2: tier-2 over 47 pages can take 5+ min — the
# user needs a count, not just per-page log lines).
files = [p for p in pages if p.is_file()]
skipped_non_files = len(pages) - len(files)
if skipped_non_files:
log(f"({skipped_non_files} non-file paths skipped)")
total = len(files)
total_written = 0
total_skipped = 0
for i, page in enumerate(files, 1):
result = process_page(
page,
force_synthetic=args.no_llm,
rebuild=args.rebuild,
peek=args.peek,
allow_egress=args.allow_egress,
progress_label=f"[{i}/{total}]",
)
total_written += len(result["written"])
total_skipped += result["skipped"]
log(f"\nDone. pages={total} chunks_written={total_written} chunks_unchanged={total_skipped}")
return EXIT_OK
if __name__ == "__main__":
sys.exit(main())
scripts/detect-transport.sh
+229
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@@ -0,0 +1,229 @@
#!/usr/bin/env bash
# detect-transport.sh — discover which vault-mutation transports are available
# on this machine, write a normalized JSON snapshot to .vault-meta/transport.json,
# and pick a preferred transport per the v1.7 fallback chain.
#
# Fallback chain (highest to lowest precedence):
# 1. cli — Obsidian CLI binary (Obsidian 1.12+). No MCP server, no TLS, no plugin.
# 2. mcp-obsidian — REST-API-backed MCP server (Local REST API plugin required).
# 3. mcpvault — Filesystem-backed MCP server (BM25 search; no Obsidian plugin).
# 4. filesystem — Direct Read/Write/Edit tools. Always available (ultimate floor).
#
# MCP auto-detection is deferred to a v1.7.x patch (calling `claude mcp list` from
# inside a running claude session has reentrancy concerns). For v1.7, we detect
# CLI + filesystem and leave MCP fields as `{"present": null, "detection": "deferred"}`.
# Users with MCP transports configured can either edit transport.json manually or
# follow the legacy guidance in wiki/references/mcp-setup.md.
#
# Usage:
# ./scripts/detect-transport.sh # detect and write .vault-meta/transport.json
# ./scripts/detect-transport.sh --peek # print result to stdout without writing
# ./scripts/detect-transport.sh --force # refresh even if existing snapshot is fresh (<7d)
# ./scripts/detect-transport.sh --quiet # suppress informational stderr output
#
# Exit codes:
# 0 — success (transport.json written or peeked)
# 2 — vault-meta/ missing and cannot be created
# 3 — unrecognized flag
set -euo pipefail
VAULT_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
META_DIR="${VAULT_ROOT}/.vault-meta"
OUTPUT_FILE="${META_DIR}/transport.json"
STALE_AFTER_DAYS=7
MODE="write"
QUIET=false
while [ $# -gt 0 ]; do
case "$1" in
--peek) MODE="peek" ;;
--force) MODE="force" ;;
--quiet) QUIET=true ;;
-h|--help)
sed -n '2,28p' "$0" | sed 's/^# \{0,1\}//'
exit 0
;;
*)
echo "ERR: unknown flag: $1" >&2
exit 3
;;
esac
shift
done
log() { $QUIET || echo "$@" >&2; }
# json_escape: read stdin and emit a JSON-encoded string (including the
# surrounding double quotes). Used for any untrusted value that lands in the
# transport.json heredoc — newlines, backslashes, control chars in upstream
# binaries (obsidian-cli --version) would otherwise break the JSON.
json_escape() {
python3 -c 'import json,sys; print(json.dumps(sys.stdin.read().strip()), end="")'
}
mkdir -p "$META_DIR" || {
echo "ERR: cannot create .vault-meta/ at $META_DIR" >&2
exit 2
}
# ── 0. Honor manual_override from existing transport.json ────────────────────
# Users can pin a non-detected transport (mcp-obsidian, mcpvault, or any custom
# value) by editing transport.json to set:
# "manual_override": true
# "preferred": "<their-choice>"
# "fallback_chain": [...]
# Auto-detection still runs (to refresh CLI/Obsidian-running flags for visibility),
# but PREFERRED and CHAIN are preserved from the existing file across both the
# normal write path AND --force runs. Documented at
# wiki/references/transport-fallback.md §Manual override.
MANUAL_OVERRIDE_FLAG=false
MANUAL_OVERRIDE_PREFERRED=""
MANUAL_OVERRIDE_CHAIN=""
if [ -f "$OUTPUT_FILE" ]; then
MANUAL_PARSE="$(python3 - "$OUTPUT_FILE" 2>/dev/null <<'PYEOF'
import json, sys
try:
with open(sys.argv[1]) as fh:
data = json.load(fh)
if data.get("manual_override") is True:
pref = data.get("preferred", "")
chain = data.get("fallback_chain", [])
# Output: line 1 = preferred; line 2 = comma-separated quoted chain entries.
print(pref)
print(",".join('"' + str(c) + '"' for c in chain))
except Exception:
pass
PYEOF
)" || MANUAL_PARSE=""
if [ -n "${MANUAL_PARSE:-}" ]; then
MANUAL_OVERRIDE_FLAG=true
MANUAL_OVERRIDE_PREFERRED="$(printf '%s\n' "$MANUAL_PARSE" | sed -n '1p')"
MANUAL_OVERRIDE_CHAIN="$(printf '%s\n' "$MANUAL_PARSE" | sed -n '2p')"
log "manual_override=true; preserving preferred=${MANUAL_OVERRIDE_PREFERRED}"
fi
fi
# ── Freshness check: skip detection if snapshot is recent ────────────────────
if [ "$MODE" = "write" ] && [ -f "$OUTPUT_FILE" ]; then
if find "$OUTPUT_FILE" -mtime -${STALE_AFTER_DAYS} -print 2>/dev/null | grep -q .; then
log "transport.json is fresh (<${STALE_AFTER_DAYS}d). Use --force to refresh."
cat "$OUTPUT_FILE"
exit 0
fi
fi
# ── 1. CLI detection ─────────────────────────────────────────────────────────
CLI_PRESENT=false
CLI_BINARY=""
CLI_VERSION=""
CLI_VERSION_RAW=""
if command -v obsidian-cli >/dev/null 2>&1; then
CLI_PRESENT=true
CLI_BINARY="obsidian-cli"
# Keep two views of the version: RAW for the human log line, JSON-escaped
# for the transport.json heredoc. CLI_VERSION below is pre-quoted (includes
# the surrounding double quotes), so the heredoc emits ${CLI_VERSION}
# without wrapping quotes.
CLI_VERSION_RAW="$(obsidian-cli --version 2>/dev/null | head -1 || echo unknown)"
CLI_VERSION="$(printf '%s' "$CLI_VERSION_RAW" | json_escape || echo '"unknown"')"
elif command -v obsidian >/dev/null 2>&1; then
# Obsidian 1.12+ ships `obsidian` as the CLI binary on some platforms.
# We treat it as cli-capable if it accepts a --cli or --version flag without launching the GUI.
if obsidian --version >/dev/null 2>&1; then
CLI_PRESENT=true
CLI_BINARY="obsidian"
CLI_VERSION_RAW="$(obsidian --version 2>/dev/null | head -1 || echo unknown)"
CLI_VERSION="$(printf '%s' "$CLI_VERSION_RAW" | json_escape || echo '"unknown"')"
fi
fi
# Fallback default when neither binary was found: must still be a valid JSON literal.
if [ -z "$CLI_VERSION" ]; then
CLI_VERSION='""'
CLI_VERSION_RAW=""
fi
# ── 2. Obsidian app running? (informational only; CLI works either way) ──────
OBSIDIAN_RUNNING=false
if command -v pgrep >/dev/null 2>&1; then
if pgrep -if 'obsidian' >/dev/null 2>&1; then
OBSIDIAN_RUNNING=true
fi
fi
# ── 3. Compute preferred + fallback chain ────────────────────────────────────
if $CLI_PRESENT; then
PREFERRED="cli"
CHAIN='"cli", "filesystem"'
else
PREFERRED="filesystem"
CHAIN='"filesystem"'
fi
# ── 3b. Apply manual_override if it was parsed from the existing snapshot ────
# Auto-detected PREFERRED/CHAIN above are overridden so the user's pinned
# transport survives every refresh cycle including --force.
if $MANUAL_OVERRIDE_FLAG; then
PREFERRED="$MANUAL_OVERRIDE_PREFERRED"
CHAIN="$MANUAL_OVERRIDE_CHAIN"
fi
# ── 4. Build JSON snapshot ───────────────────────────────────────────────────
TIMESTAMP="$(date -u +%Y-%m-%dT%H:%M:%SZ)"
HOSTNAME="$(hostname 2>/dev/null || echo unknown)"
snapshot() {
cat <<JSON
{
"schema_version": 1,
"detected_at": "${TIMESTAMP}",
"host": "${HOSTNAME}",
"vault_root": "${VAULT_ROOT}",
"manual_override": ${MANUAL_OVERRIDE_FLAG},
"preferred": "${PREFERRED}",
"fallback_chain": [${CHAIN}],
"available": {
"cli": {
"present": ${CLI_PRESENT},
"binary": "${CLI_BINARY}",
"version_string": ${CLI_VERSION},
"obsidian_app_running": ${OBSIDIAN_RUNNING}
},
"filesystem": {
"present": true,
"vault_root": "${VAULT_ROOT}",
"note": "ultimate fallback; uses Claude's Read/Write/Edit tools directly"
},
"mcp_obsidian": {
"present": null,
"detection": "deferred",
"note": "v1.7 does not auto-detect MCP servers. Configure manually per wiki/references/mcp-setup.md and edit this file by hand if needed."
},
"mcpvault": {
"present": null,
"detection": "deferred",
"note": "v1.7 does not auto-detect MCP servers. Configure manually per wiki/references/mcp-setup.md and edit this file by hand if needed."
}
}
}
JSON
}
if [ "$MODE" = "peek" ]; then
snapshot
exit 0
fi
# Atomic write: stage to .tmp then rename. Avoids partial files if killed mid-write.
TMP="${OUTPUT_FILE}.$$.tmp"
trap 'rm -f "$TMP"' EXIT
snapshot > "$TMP"
mv "$TMP" "$OUTPUT_FILE"
trap - EXIT
log "Wrote: ${OUTPUT_FILE}"
log "Preferred transport: ${PREFERRED}"
$CLI_PRESENT && log " CLI: ${CLI_BINARY} (${CLI_VERSION_RAW})"
log " Filesystem: always available (Read/Write/Edit tools)"
log " MCP: not auto-detected (see wiki/references/mcp-setup.md to configure)"
scripts/rerank.py
+312
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@@ -0,0 +1,312 @@
#!/usr/bin/env python3
"""rerank.py — query-time reranker for chunk candidates.
Takes a query string + a list of candidate chunks (from BM25, vector, or any
upstream stage) and reorders them using semantic similarity.
v1.7 strategy (in preference order, automatically chosen at runtime):
1. If ollama is reachable AND nomic-embed-text is pulled
→ embed the query, embed each candidate's contextualized_text,
rank by cosine. Caches per-chunk embeddings in
.vault-meta/embed-cache.json keyed by body_hash.
2. Otherwise
→ no-op rerank: return candidates in input order with a synthesized
note. Caller (retrieve.py) still gets a useful result; downstream
drill-into-page logic is unchanged.
Future v1.7.x upgrade paths:
- Cross-encoder reranker (sentence-transformers BGE-base) if installed
- Cohere Rerank API if COHERE_API_KEY set
- Voyage Rerank API if VOYAGE_API_KEY set
Mirrors the localhost-only OLLAMA_URL guard from scripts/tiling-check.py:
remote ollama endpoints require --allow-remote-ollama because page bodies
are POSTed as embedding input.
Usage:
rerank.py "query string" --candidates candidates.json [--top 5]
rerank.py "query string" --candidates - --top 5 # stdin
rerank.py --peek "query string" # show strategy chosen
Candidates JSON shape:
[{"chunk_id": "c-000042:3", "path": ".vault-meta/chunks/.../chunk-003.json", "score": 7.1}, ...]
Output: ranked candidates with `rerank_score` added.
Exit codes:
0 — success
2 — usage error
3 — candidate input malformed
10 — ollama unreachable (no-op rerank performed, exit 0 with note)
11 — model not pulled (no-op rerank performed, exit 0 with note)
"""
import argparse
import fcntl
import json
import math
import os
import shutil
import sys
import time
import urllib.error
import urllib.parse
import urllib.request
from datetime import datetime, timezone
from pathlib import Path
VAULT_ROOT = Path(__file__).resolve().parent.parent
META_DIR = VAULT_ROOT / ".vault-meta"
EMBED_CACHE_PATH = META_DIR / "embed-cache.json"
CACHE_LOCK = META_DIR / ".embed-cache.lock"
DEFAULT_OLLAMA_URL = "http://127.0.0.1:11434"
DEFAULT_MODEL = "nomic-embed-text"
OLLAMA_TIMEOUT_SEC = 3
EMBED_TIMEOUT_SEC = 30
MAX_RESPONSE_BYTES = 4 * 1024 * 1024
EXIT_OK = 0
EXIT_USAGE = 2
EXIT_CANDIDATES = 3
EXIT_NO_OLLAMA = 10
EXIT_NO_MODEL = 11
def log(msg):
print(msg, file=sys.stderr)
def cosine(a, b):
if not a or not b or len(a) != len(b):
return 0.0
dot = sum(x * y for x, y in zip(a, b))
na = math.sqrt(sum(x * x for x in a))
nb = math.sqrt(sum(y * y for y in b))
if na == 0 or nb == 0:
return 0.0
return dot / (na * nb)
def ollama_url(allow_remote):
url = os.environ.get("OLLAMA_URL", DEFAULT_OLLAMA_URL).rstrip("/")
if not allow_remote:
parsed = urllib.parse.urlparse(url)
host = parsed.hostname or ""
if host not in ("127.0.0.1", "localhost", "::1"):
log(f"ERR: OLLAMA_URL={url} points off-localhost (host={host!r}).")
log(" Either: (a) run ollama locally — `systemctl --user start ollama` or `ollama serve`")
log(" Or: (b) pass --allow-remote-ollama through retrieve.py, which forwards it here.")
log(" Or: (c) unset OLLAMA_URL to fall back to the local default (127.0.0.1:11434).")
sys.exit(EXIT_USAGE)
return url
def ollama_alive(url):
try:
req = urllib.request.Request(f"{url}/api/tags", method="GET")
with urllib.request.urlopen(req, timeout=OLLAMA_TIMEOUT_SEC) as resp:
data = json.loads(resp.read(MAX_RESPONSE_BYTES))
models = [m.get("name", "").split(":")[0] for m in data.get("models", [])]
return True, models
except (urllib.error.URLError, json.JSONDecodeError, OSError):
return False, []
def embed_one(url, model, text):
payload = json.dumps({"model": model, "prompt": text}).encode("utf-8")
req = urllib.request.Request(
f"{url}/api/embeddings",
data=payload,
headers={"Content-Type": "application/json"},
method="POST",
)
with urllib.request.urlopen(req, timeout=EMBED_TIMEOUT_SEC) as resp:
data = json.loads(resp.read(MAX_RESPONSE_BYTES))
return data.get("embedding") or []
def load_cache():
if not EMBED_CACHE_PATH.is_file():
return {}
try:
return json.loads(EMBED_CACHE_PATH.read_text(encoding="utf-8"))
except (json.JSONDecodeError, OSError):
return {}
def save_cache(cache):
"""Persist the embed cache atomically.
v1.7.2 / closes audit M7: previously used blocking fcntl.LOCK_EX with no
timeout, which could hang indefinitely on a non-flock-capable filesystem
(some NFS mounts, network shares, FUSE backends without lock support).
Now uses LOCK_NB with a 3-attempt retry loop, then falls back to writing
without the lock (with a WARN) so the rerank pipeline never hangs the
user's session. The temp + os.replace pattern provides write atomicity
even without the lock; the lock only serializes concurrent writers.
"""
META_DIR.mkdir(parents=True, exist_ok=True)
fd = os.open(str(CACHE_LOCK), os.O_CREAT | os.O_WRONLY, 0o644)
locked = False
try:
for attempt in range(3):
try:
fcntl.flock(fd, fcntl.LOCK_EX | fcntl.LOCK_NB)
locked = True
break
except BlockingIOError:
time.sleep(0.1)
if not locked:
msg = ("WARN: rerank embed-cache lock unavailable after 3 tries; "
"writing unlocked (atomic via temp+rename). Concurrent writers "
"may overwrite each other's last update.")
log(msg)
# v1.9.1 / closes audit Data M1: also route to .vault-meta/hook.log so
# the user sees the event via wiki-lint (stderr alone is invisible to
# most callers; this matches the hook's logging shape).
try:
META_DIR.mkdir(parents=True, exist_ok=True)
hook_log = META_DIR / "hook.log"
ts = datetime.now(timezone.utc).strftime("%Y-%m-%dT%H:%M:%SZ")
with hook_log.open("a", encoding="utf-8") as fh:
fh.write(f"{ts} rerank embed-cache lock unavailable; wrote unlocked\n")
except OSError:
pass # never block on a logging failure
tmp = EMBED_CACHE_PATH.with_suffix(f".{os.getpid()}.tmp")
tmp.write_text(json.dumps(cache, ensure_ascii=False), encoding="utf-8")
os.replace(tmp, EMBED_CACHE_PATH)
finally:
if locked:
try:
fcntl.flock(fd, fcntl.LOCK_UN)
except OSError:
pass
os.close(fd)
def load_chunk(chunk_rel_path):
p = VAULT_ROOT / chunk_rel_path
if not p.is_file():
return None
try:
return json.loads(p.read_text(encoding="utf-8"))
except (json.JSONDecodeError, OSError):
return None
def rerank(query, candidates, top_k=5, allow_remote=False):
"""Returns candidates list, possibly truncated to top_k, with rerank_score added.
Falls back to input-order if ollama is unavailable (still adds rerank_source: 'noop').
"""
url = ollama_url(allow_remote)
alive, models = ollama_alive(url)
if not alive:
log("ollama unreachable — no-op rerank")
for c in candidates:
c["rerank_score"] = float(c.get("score", 0.0))
c["rerank_source"] = "noop-no-ollama"
return candidates[:top_k]
if DEFAULT_MODEL not in models:
log(f"model {DEFAULT_MODEL} not pulled — no-op rerank")
for c in candidates:
c["rerank_score"] = float(c.get("score", 0.0))
c["rerank_source"] = "noop-no-model"
return candidates[:top_k]
cache = load_cache()
cache_dirty = False
try:
q_emb = embed_one(url, DEFAULT_MODEL, query)
except Exception as e:
log(f"query embed failed: {e}")
for c in candidates:
c["rerank_score"] = float(c.get("score", 0.0))
c["rerank_source"] = "noop-embed-error"
return candidates[:top_k]
for c in candidates:
chunk = load_chunk(c.get("path", ""))
if not chunk:
c["rerank_score"] = 0.0
c["rerank_source"] = "missing-chunk"
continue
body_hash = chunk.get("body_hash", "")
cache_key = f"{DEFAULT_MODEL}:{body_hash}"
emb = cache.get(cache_key)
if not emb:
text = chunk.get("contextualized_text") or chunk.get("raw_text", "")
try:
emb = embed_one(url, DEFAULT_MODEL, text)
except Exception as e:
log(f"embed failed for {c.get('chunk_id')}: {e}")
c["rerank_score"] = float(c.get("score", 0.0))
c["rerank_source"] = "embed-error"
continue
cache[cache_key] = emb
cache_dirty = True
c["rerank_score"] = cosine(q_emb, emb)
c["rerank_source"] = f"cosine:{DEFAULT_MODEL}"
if cache_dirty:
save_cache(cache)
ranked = sorted(candidates, key=lambda x: x.get("rerank_score", 0.0), reverse=True)
return ranked[:top_k]
def main():
parser = argparse.ArgumentParser(description="Rerank chunk candidates by semantic similarity.")
parser.add_argument("query", nargs="?", help="Query text")
parser.add_argument("--candidates", help="Path to candidates JSON or `-` for stdin",
default=None)
parser.add_argument("--top", type=int, default=5, help="Top-K to return")
parser.add_argument("--peek", action="store_true",
help="Print rerank strategy chosen and exit")
parser.add_argument("--allow-remote-ollama", action="store_true",
help="Accept non-localhost OLLAMA_URL (potential data exfil)")
args = parser.parse_args()
if args.peek:
if not args.query:
log("--peek needs a query string")
sys.exit(EXIT_USAGE)
url = ollama_url(args.allow_remote_ollama)
alive, models = ollama_alive(url)
strategy = "noop-no-ollama"
if alive:
strategy = f"cosine:{DEFAULT_MODEL}" if DEFAULT_MODEL in models else "noop-no-model"
print(json.dumps({
"query": args.query,
"strategy": strategy,
"ollama_url": url,
"ollama_alive": alive,
"model_present": DEFAULT_MODEL in models,
"checked_at": datetime.now(timezone.utc).strftime("%Y-%m-%dT%H:%M:%SZ"),
}, indent=2))
return EXIT_OK
if not args.query or args.candidates is None:
log("usage: rerank.py <query> --candidates <path|-> [--top N]")
return EXIT_USAGE
if args.candidates == "-":
cand_text = sys.stdin.read()
else:
cand_text = Path(args.candidates).read_text(encoding="utf-8")
try:
candidates = json.loads(cand_text)
if not isinstance(candidates, list):
raise ValueError("candidates must be a JSON list")
except (json.JSONDecodeError, ValueError) as e:
log(f"ERR: bad candidates JSON: {e}")
return EXIT_CANDIDATES
result = rerank(args.query, candidates, top_k=args.top,
allow_remote=args.allow_remote_ollama)
print(json.dumps(result, indent=2))
return EXIT_OK
if __name__ == "__main__":
sys.exit(main())
scripts/retrieve.py
+195
View File
@@ -0,0 +1,195 @@
#!/usr/bin/env python3
"""retrieve.py — hybrid retrieval orchestrator for the Compound Vault.
Pipeline (v1.7):
query → bm25-index.py query (top-K candidates by BM25 over contextualized chunks)
→ rerank.py (cosine on nomic-embed-text vectors via ollama,
or no-op if ollama unavailable)
→ drill (return chunk pages with absolute paths so the
caller can Read them and synthesize)
Loads sibling scripts as Python modules (no subprocess overhead). Falls back
gracefully when index or rerank stage is missing:
- If .vault-meta/bm25/index.json is absent → exit 10 with friendly message;
caller falls back to v1.6 legacy
hot→index→drill read order.
- If .vault-meta/chunks/ is empty → exit 10 (same).
- If rerank stage cannot embed (no ollama) → no-op rerank, returns BM25 order.
Output schema (JSON to stdout):
{
"query": "...",
"strategy": "bm25+rerank:cosine:nomic-embed-text" | "bm25+noop-rerank",
"top_k": 5,
"candidates": [
{
"chunk_id": "c-000042:3",
"page_address": "c-000042",
"page_path": "wiki/concepts/Foo.md",
"absolute_path": "/abs/path/to/wiki/concepts/Foo.md",
"chunk_index": 3,
"bm25_score": 7.12,
"rerank_score": 0.81,
"rerank_source": "cosine:nomic-embed-text",
"snippet": "... first 200 chars of the chunk ..."
},
...
]
}
Usage:
retrieve.py "your query here" # standard: BM25 top-20, rerank to top-5
retrieve.py "query" --top 10 # change result count
retrieve.py "query" --no-rerank # skip rerank, BM25-only
retrieve.py "query" --explain # include per-stage diagnostics
Exit codes:
0 — success
2 — usage error
10 — feature not provisioned (no chunks or no BM25 index); caller falls back
"""
import argparse
import importlib.util
import json
import sys
from pathlib import Path
VAULT_ROOT = Path(__file__).resolve().parent.parent
SCRIPTS_DIR = VAULT_ROOT / "scripts"
META_DIR = VAULT_ROOT / ".vault-meta"
CHUNKS_DIR = META_DIR / "chunks"
BM25_INDEX = META_DIR / "bm25" / "index.json"
EXIT_OK = 0
EXIT_USAGE = 2
EXIT_NOT_PROVISIONED = 10
def log(msg):
print(msg, file=sys.stderr)
def import_sibling(name, filename):
"""Import a hyphenated sibling .py file as a Python module.
Wrapped in try/except (v1.7.2; closes audit M5) so a syntax error or
missing dependency in a sibling helper produces a friendly diagnostic
instead of a bare Python traceback at the user's first retrieve call.
"""
target = SCRIPTS_DIR / filename
if not target.is_file():
log(f"ERR: sibling helper {filename} not found at {target}")
log(" Run `bash bin/setup-retrieve.sh --check` to verify the install.")
sys.exit(EXIT_NOT_PROVISIONED)
try:
spec = importlib.util.spec_from_file_location(name, target)
mod = importlib.util.module_from_spec(spec)
spec.loader.exec_module(mod)
return mod
except (ImportError, SyntaxError, AttributeError) as e:
log(f"ERR: failed to import sibling helper {filename}: {type(e).__name__}: {e}")
log(" This likely means the helper script is corrupted or has a syntax error.")
log(" Run `python3 scripts/<helper>.py --help` directly to see the underlying error.")
log(" If it persists: re-clone the repo or check `git status` for local damage.")
sys.exit(EXIT_NOT_PROVISIONED)
def chunk_snippet(chunk_data, max_chars=200):
text = chunk_data.get("raw_text", "")
if len(text) <= max_chars:
return text
return text[:max_chars].rstrip() + "…"
def main():
parser = argparse.ArgumentParser(description="Hybrid retrieval over the vault.")
parser.add_argument("query", help="Natural-language query")
parser.add_argument("--top", type=int, default=5, help="Final result count (post-rerank)")
parser.add_argument("--bm25-top", type=int, default=20,
help="Candidate count from BM25 (pre-rerank)")
parser.add_argument("--no-rerank", action="store_true",
help="Skip the rerank stage; return BM25-only")
parser.add_argument("--explain", action="store_true",
help="Include per-stage diagnostics in output")
parser.add_argument("--allow-remote-ollama", action="store_true",
help="Forwarded to rerank.py")
args = parser.parse_args()
if not BM25_INDEX.is_file():
log(f"ERR: no BM25 index at {BM25_INDEX}. Run `bash bin/setup-retrieve.sh` "
"to provision, or fall back to legacy hot→index→drill.")
return EXIT_NOT_PROVISIONED
if not CHUNKS_DIR.is_dir() or not any(CHUNKS_DIR.iterdir()):
log(f"ERR: no chunks at {CHUNKS_DIR}. Run "
"`python3 scripts/contextual-prefix.py --all` first.")
return EXIT_NOT_PROVISIONED
bm25 = import_sibling("bm25_index", "bm25-index.py")
reranker = import_sibling("rerank", "rerank.py")
bm25_hits = bm25.query(args.query, top_k=args.bm25_top)
log(f"bm25: {len(bm25_hits)} hits")
candidates = []
for h in bm25_hits:
chunk_path = VAULT_ROOT / h["path"]
try:
chunk = json.loads(chunk_path.read_text(encoding="utf-8"))
except (json.JSONDecodeError, OSError):
continue
candidates.append({
"chunk_id": h["chunk_id"],
"page_address": chunk.get("page_address"),
"page_path": chunk.get("page_path"),
"absolute_path": str((VAULT_ROOT / chunk.get("page_path", "")).resolve()),
"chunk_index": chunk.get("chunk_index"),
"bm25_score": h["score"],
"path": h["path"],
"snippet": chunk_snippet(chunk),
})
if args.no_rerank:
final = candidates[:args.top]
strategy = "bm25-only"
for c in final:
c["rerank_score"] = c["bm25_score"]
c["rerank_source"] = "skipped"
else:
final = reranker.rerank(
args.query, candidates, top_k=args.top,
allow_remote=args.allow_remote_ollama,
)
# Derive strategy from first candidate's rerank_source
first_src = (final[0].get("rerank_source") if final else "unknown")
strategy = f"bm25+rerank:{first_src}"
# Dedupe by page (we may have multiple chunks of the same page; collapse to best)
by_page = {}
for c in final:
addr = c.get("page_address")
if addr not in by_page or c.get("rerank_score", 0) > by_page[addr].get("rerank_score", 0):
by_page[addr] = c
deduped = list(by_page.values())
deduped.sort(key=lambda c: c.get("rerank_score", 0), reverse=True)
out = {
"query": args.query,
"strategy": strategy,
"top_k": args.top,
"candidates": deduped[:args.top],
}
if args.explain:
out["explain"] = {
"bm25_candidate_count": len(bm25_hits),
"post_rerank_count": len(final),
"deduped_count": len(deduped),
"bm25_top_param": args.bm25_top,
}
print(json.dumps(out, indent=2, ensure_ascii=False))
return EXIT_OK
if __name__ == "__main__":
sys.exit(main())
scripts/tiling-check.py
+496
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@@ -0,0 +1,496 @@
#!/usr/bin/env python3
"""tiling-check.py — DragonScale Mechanism 3: semantic tiling lint.
Computes per-page embeddings via a local ollama instance and reports
candidate duplicate page pairs. Read-only; never modifies wiki pages.
Security model:
- Defaults to http://127.0.0.1:11434. Remote ollama endpoints require
--allow-remote-ollama explicitly (vault bodies are POSTed as embedding
input; a hostile env var would otherwise exfiltrate content).
- Rejects symlinked page files to prevent escape outside the vault root.
Feature-gated: exits 10 if ollama is unreachable or 11 if the embedding
model is not pulled, so the calling skill can no-op gracefully. Exits 0
on success. Exit 3 on cache corruption. Exit 2 on usage error.
Concurrency:
- Locks `.vault-meta/.tiling.lock` (flock exclusive) around cache I/O.
- Per-PID temp file to avoid shared-tempfile races.
Usage:
tiling-check.py # run; exit 10/11 if ollama/model missing
tiling-check.py --report PATH # also write report to PATH
tiling-check.py --rebuild-cache # ignore cached embeddings
tiling-check.py --peek # structured diagnostics; no compute
tiling-check.py --allow-remote-ollama # accept non-localhost OLLAMA_URL
"""
import argparse
import fcntl
import hashlib
import json
import math
import os
import re
import sys
import urllib.error
import urllib.parse
import urllib.request
from datetime import datetime
from pathlib import Path
DEFAULT_OLLAMA_URL = "http://127.0.0.1:11434"
DEFAULT_MODEL = "nomic-embed-text"
OLLAMA_TIMEOUT_SEC = 3
EMBED_TIMEOUT_SEC = 30
MAX_RESPONSE_BYTES = 4 * 1024 * 1024 # 4 MB; embeddings can be ~10 KB each
VAULT_ROOT = Path(__file__).resolve().parent.parent
WIKI_DIR = VAULT_ROOT / "wiki"
META_DIR = VAULT_ROOT / ".vault-meta"
CACHE_PATH = META_DIR / "tiling-cache.json"
CACHE_LOCK = META_DIR / ".tiling.lock"
THRESHOLDS_PATH = META_DIR / "tiling-thresholds.json"
EXCLUDE_TYPES = {"meta", "fold"}
EXCLUDE_FILENAMES = {
"_index.md", "index.md", "log.md", "hot.md", "overview.md",
"dashboard.md", "Wiki Map.md", "getting-started.md",
}
EXCLUDE_PATH_PREFIXES = ("wiki/folds/", "wiki/meta/")
MAX_BODY_BYTES = 128 * 1024
SCALE_WARN_PAGES = 500
SCALE_HARD_FAIL_PAGES = 5000
EXIT_OK = 0
EXIT_USAGE = 2
EXIT_CACHE_CORRUPT = 3
EXIT_SCALE_EXCEEDED = 4
EXIT_NO_OLLAMA = 10
EXIT_NO_MODEL = 11
FRONTMATTER_RE = re.compile(r"^---\n(.*?)\n---\n", re.DOTALL)
TYPE_RE = re.compile(r"^type:\s*(\S+)", re.MULTILINE)
def log(msg: str) -> None:
print(msg, file=sys.stderr)
def _is_local_url(url: str) -> bool:
try:
host = urllib.parse.urlparse(url).hostname or ""
except ValueError:
return False
return host in ("127.0.0.1", "localhost", "::1")
def _http_get_json(url: str, timeout: float) -> dict:
with urllib.request.urlopen(url, timeout=timeout) as resp:
raw = resp.read(MAX_RESPONSE_BYTES + 1)
if len(raw) > MAX_RESPONSE_BYTES:
raise RuntimeError("response exceeded size limit")
return json.loads(raw.decode("utf-8"))
def _http_post_json(url: str, payload: dict, timeout: float) -> dict:
data = json.dumps(payload).encode("utf-8")
req = urllib.request.Request(url, data=data, headers={"Content-Type": "application/json"})
with urllib.request.urlopen(req, timeout=timeout) as resp:
raw = resp.read(MAX_RESPONSE_BYTES + 1)
if len(raw) > MAX_RESPONSE_BYTES:
raise RuntimeError("response exceeded size limit")
return json.loads(raw.decode("utf-8"))
def detect_ollama(url: str) -> bool:
try:
_http_get_json(f"{url}/api/version", OLLAMA_TIMEOUT_SEC)
return True
except (urllib.error.URLError, OSError, ValueError, TimeoutError, RuntimeError):
return False
def detect_model(url: str, model: str) -> bool:
try:
data = _http_get_json(f"{url}/api/tags", OLLAMA_TIMEOUT_SEC)
except (urllib.error.URLError, OSError, ValueError, TimeoutError, RuntimeError):
return False
models = data.get("models")
if not isinstance(models, list):
return False
for entry in models:
if not isinstance(entry, dict):
continue
name = entry.get("name", "")
if isinstance(name, str) and (name == model or name.startswith(f"{model}:")):
return True
return False
def parse_frontmatter(text: str) -> tuple[dict, str]:
m = FRONTMATTER_RE.match(text)
if not m:
return {}, text
fm_raw = m.group(1)
body = text[m.end():]
fm: dict = {}
tm = TYPE_RE.search(fm_raw)
if tm:
fm["type"] = tm.group(1).strip().strip('"').strip("'")
return fm, body
def body_hash(body: str, model: str) -> str:
h = hashlib.sha256()
h.update(f"model={model}\n".encode("utf-8"))
h.update(body.encode("utf-8"))
return h.hexdigest()
def cosine(a: list[float], b: list[float]) -> float:
if len(a) != len(b):
raise ValueError(f"dim mismatch: {len(a)} vs {len(b)}")
dot = sum(x * y for x, y in zip(a, b))
na = math.sqrt(sum(x * x for x in a))
nb = math.sqrt(sum(x * x for x in b))
if na == 0.0 or nb == 0.0:
return 0.0
return dot / (na * nb)
def _lock_cache():
META_DIR.mkdir(exist_ok=True)
fd = os.open(str(CACHE_LOCK), os.O_CREAT | os.O_RDWR, 0o644)
try:
fcntl.flock(fd, fcntl.LOCK_EX)
except OSError:
os.close(fd)
raise
return fd
def _unlock_cache(fd: int) -> None:
try:
fcntl.flock(fd, fcntl.LOCK_UN)
finally:
os.close(fd)
def load_cache(current_model: str) -> dict:
if not CACHE_PATH.exists():
return {"version": 1, "model": current_model, "embeddings": {}}
try:
with CACHE_PATH.open() as f:
data = json.load(f)
except (OSError, json.JSONDecodeError) as exc:
log(f"ERR: cache read failed: {exc}")
sys.exit(EXIT_CACHE_CORRUPT)
if data.get("version") != 1:
log(f"ERR: unknown cache version: {data.get('version')}")
sys.exit(EXIT_CACHE_CORRUPT)
cached_model = data.get("model", "")
if cached_model != current_model:
log(f"INFO: cached model '{cached_model}' differs from current '{current_model}'; invalidating cache")
return {"version": 1, "model": current_model, "embeddings": {}}
if not isinstance(data.get("embeddings"), dict):
log("ERR: cache.embeddings is not a dict")
sys.exit(EXIT_CACHE_CORRUPT)
return data
def save_cache(cache: dict) -> None:
META_DIR.mkdir(exist_ok=True)
tmp = CACHE_PATH.with_name(f"{CACHE_PATH.stem}.{os.getpid()}.tmp")
with tmp.open("w") as f:
json.dump(cache, f, indent=2)
tmp.replace(CACHE_PATH)
def load_thresholds() -> dict:
if not THRESHOLDS_PATH.exists():
return {
"version": 1, "model": DEFAULT_MODEL,
"bands": {"error": 0.90, "review": 0.80},
"calibrated": False, "calibration_pairs_labeled": 0,
}
with THRESHOLDS_PATH.open() as f:
return json.load(f)
def included(path: Path, fm: dict) -> tuple[bool, str]:
rel = path.relative_to(VAULT_ROOT).as_posix()
if path.is_symlink():
return False, "symlink"
resolved = path.resolve()
try:
resolved.relative_to(VAULT_ROOT.resolve())
except ValueError:
return False, "escapes vault"
if path.name in EXCLUDE_FILENAMES:
return False, "excluded filename"
for prefix in EXCLUDE_PATH_PREFIXES:
if rel.startswith(prefix):
return False, f"under {prefix}"
if fm.get("type") in EXCLUDE_TYPES:
return False, f"type={fm['type']}"
return True, "included"
def embed(text: str, model: str, url: str) -> list[float]:
data = _http_post_json(
f"{url}/api/embeddings",
{"model": model, "prompt": text},
EMBED_TIMEOUT_SEC,
)
emb = data.get("embedding")
if not isinstance(emb, list) or not emb:
raise RuntimeError(f"ollama returned no embedding: {str(data)[:200]}")
for v in emb:
if not isinstance(v, (int, float)):
raise RuntimeError("embedding contains non-numeric values")
return emb
def run_check(
rebuild: bool,
report_path: Path | None,
ollama_url: str,
model: str,
) -> int:
if not detect_ollama(ollama_url):
log(f"ollama not reachable at {ollama_url}; skipping tiling check")
return EXIT_NO_OLLAMA
if not detect_model(ollama_url, model):
log(f"model '{model}' not pulled; run: ollama pull {model}")
return EXIT_NO_MODEL
thresholds = load_thresholds()
lock_fd = _lock_cache()
try:
cache = (load_cache(model) if not rebuild
else {"version": 1, "model": model, "embeddings": {}})
pages: list[tuple[str, list[float]]] = []
scanned = 0
computed = 0
cached_hits = 0
skipped_counts: dict[str, int] = {}
live_paths: set[str] = set()
candidates = sorted(WIKI_DIR.rglob("*.md"))
scale_n = len(candidates)
if scale_n > SCALE_HARD_FAIL_PAGES:
log(f"ERR: {scale_n} pages exceed hard-fail limit {SCALE_HARD_FAIL_PAGES}")
return EXIT_SCALE_EXCEEDED
if scale_n > SCALE_WARN_PAGES:
log(f"WARN: {scale_n} pages; cold-cache embed will issue ~{scale_n} POSTs to ollama")
for md in candidates:
scanned += 1
# Symlink and vault-root guards must run BEFORE read_text so a
# hostile symlink cannot cause off-vault content to be read and
# POSTed to the embedding endpoint.
if md.is_symlink():
skipped_counts["symlink"] = skipped_counts.get("symlink", 0) + 1
continue
try:
resolved = md.resolve(strict=True)
resolved.relative_to(VAULT_ROOT.resolve())
except (OSError, ValueError):
skipped_counts["escapes vault"] = skipped_counts.get("escapes vault", 0) + 1
continue
try:
text = md.read_text(encoding="utf-8")
except (OSError, UnicodeDecodeError):
skipped_counts["read_error"] = skipped_counts.get("read_error", 0) + 1
continue
if len(text.encode("utf-8")) > MAX_BODY_BYTES:
skipped_counts["too_large"] = skipped_counts.get("too_large", 0) + 1
continue
fm, body = parse_frontmatter(text)
ok, reason = included(md, fm)
if not ok:
skipped_counts[reason] = skipped_counts.get(reason, 0) + 1
continue
rel = md.relative_to(VAULT_ROOT).as_posix()
live_paths.add(rel)
h = body_hash(body, model)
entry = cache["embeddings"].get(rel)
if entry and entry.get("hash") == h:
pages.append((rel, entry["embedding"]))
cached_hits += 1
continue
try:
emb = embed(body, model, ollama_url)
except Exception as exc:
log(f"ERR embedding {rel}: {exc}")
skipped_counts["embed_error"] = skipped_counts.get("embed_error", 0) + 1
continue
cache["embeddings"][rel] = {
"hash": h,
"embedding": emb,
"computed_at": datetime.utcnow().isoformat(timespec="seconds") + "Z",
}
pages.append((rel, emb))
computed += 1
# Orphan GC: drop cache entries for paths that no longer exist.
orphans = [k for k in cache["embeddings"] if k not in live_paths]
for k in orphans:
del cache["embeddings"][k]
save_cache(cache)
finally:
_unlock_cache(lock_fd)
review = thresholds["bands"]["review"]
error_ = thresholds["bands"]["error"]
pairs: list[tuple[float, str, str]] = []
for i in range(len(pages)):
for j in range(i + 1, len(pages)):
a_path, a_emb = pages[i]
b_path, b_emb = pages[j]
try:
sim = cosine(a_emb, b_emb)
except ValueError as exc:
log(f"WARN cosine skip ({a_path}, {b_path}): {exc}")
continue
if sim >= review:
pairs.append((sim, a_path, b_path))
pairs.sort(reverse=True)
errors = [p for p in pairs if p[0] >= error_]
reviews = [p for p in pairs if review <= p[0] < error_]
out_lines: list[str] = []
out_lines.append("# Semantic Tiling Report")
out_lines.append("")
out_lines.append(f"- generated: {datetime.utcnow().isoformat(timespec='seconds')}Z")
out_lines.append(f"- model: {model}")
out_lines.append(f"- ollama_url: {ollama_url}")
out_lines.append(f"- thresholds: error>={error_}, review={review}-{error_}")
out_lines.append(f"- calibrated: {thresholds.get('calibrated', False)}"
+ (" (using uncalibrated defaults)" if not thresholds.get("calibrated") else ""))
out_lines.append(f"- pages scanned: {scanned}; embedded: {len(pages)}; skipped: {sum(skipped_counts.values())}")
if skipped_counts:
out_lines.append("- skipped reasons: " + ", ".join(f"{k}={v}" for k, v in sorted(skipped_counts.items())))
out_lines.append(f"- cache hits: {cached_hits}; recomputed: {computed}; orphans pruned: {len(orphans)}")
out_lines.append("")
out_lines.append(f"## Errors (similarity >= {error_})")
out_lines.append("")
if not errors:
out_lines.append("- none")
else:
for sim, a, b in errors:
out_lines.append(f"- `{sim:.4f}` {a} -- {b}")
out_lines.append("")
out_lines.append(f"## Review ({review} <= similarity < {error_})")
out_lines.append("")
if not reviews:
out_lines.append("- none")
else:
for sim, a, b in reviews:
out_lines.append(f"- `{sim:.4f}` {a} -- {b}")
report = "\n".join(out_lines) + "\n"
print(report)
if report_path is not None:
# Confine report writes to VAULT_ROOT. A path that resolves outside
# the vault is refused (prevents `--report /etc/passwd` style
# accidents or hostile args from writing outside the repo).
try:
resolved_report = (
report_path if report_path.is_absolute() else (Path.cwd() / report_path)
).resolve()
resolved_report.relative_to(VAULT_ROOT.resolve())
except ValueError:
log(f"ERR: --report path '{report_path}' escapes vault root {VAULT_ROOT}")
return EXIT_USAGE
resolved_report.parent.mkdir(parents=True, exist_ok=True)
resolved_report.write_text(report, encoding="utf-8")
log(f"report written: {resolved_report}")
return EXIT_OK
def cmd_peek(ollama_url: str, model: str) -> int:
"""Structured diagnostics. Prints a JSON object and a plain summary."""
diag: dict = {}
script_path = Path(__file__).resolve()
diag["script_path"] = str(script_path)
diag["script_executable"] = os.access(script_path, os.X_OK)
diag["python"] = sys.executable
diag["vault_root"] = str(VAULT_ROOT)
diag["ollama_url"] = ollama_url
diag["ollama_reachable"] = detect_ollama(ollama_url)
diag["model_requested"] = model
diag["model_present"] = detect_model(ollama_url, model) if diag["ollama_reachable"] else False
diag["cache_present"] = CACHE_PATH.exists()
diag["cache_readable"] = False
diag["cache_entries"] = 0
diag["cache_model"] = None
if diag["cache_present"]:
try:
with CACHE_PATH.open() as f:
c = json.load(f)
diag["cache_readable"] = (c.get("version") == 1
and isinstance(c.get("embeddings"), dict))
diag["cache_entries"] = len(c.get("embeddings", {}))
diag["cache_model"] = c.get("model")
except (OSError, json.JSONDecodeError) as exc:
diag["cache_readable"] = False
diag["cache_error"] = str(exc)
diag["thresholds_present"] = THRESHOLDS_PATH.exists()
diag["thresholds_readable"] = False
if diag["thresholds_present"]:
try:
with THRESHOLDS_PATH.open() as f:
t = json.load(f)
diag["thresholds_readable"] = True
diag["thresholds_calibrated"] = bool(t.get("calibrated", False))
diag["thresholds_bands"] = t.get("bands", {})
except (OSError, json.JSONDecodeError):
diag["thresholds_readable"] = False
print(json.dumps(diag, indent=2))
if not diag["ollama_reachable"]:
return EXIT_NO_OLLAMA
if not diag["model_present"]:
return EXIT_NO_MODEL
if diag["cache_present"] and not diag["cache_readable"]:
return EXIT_CACHE_CORRUPT
return EXIT_OK
def main(argv: list[str]) -> int:
p = argparse.ArgumentParser()
p.add_argument("--report", type=Path, default=None)
p.add_argument("--rebuild-cache", action="store_true")
p.add_argument("--peek", action="store_true")
p.add_argument("--allow-remote-ollama", action="store_true",
help="allow OLLAMA_URL env override pointing outside localhost")
p.add_argument("--model", default=DEFAULT_MODEL)
args = p.parse_args(argv)
env_url = os.environ.get("OLLAMA_URL")
ollama_url = env_url or DEFAULT_OLLAMA_URL
if env_url and not _is_local_url(ollama_url) and not args.allow_remote_ollama:
log(f"ERR: OLLAMA_URL={ollama_url!r} is not localhost. "
f"Vault content would be POSTed to a non-local host. "
f"Pass --allow-remote-ollama to override.")
return EXIT_USAGE
if args.peek:
return cmd_peek(ollama_url, args.model)
return run_check(
rebuild=args.rebuild_cache,
report_path=args.report,
ollama_url=ollama_url,
model=args.model,
)
if __name__ == "__main__":
sys.exit(main(sys.argv[1:]))
scripts/wiki-lock.sh
+341
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@@ -0,0 +1,341 @@
#!/usr/bin/env bash
# wiki-lock.sh — per-file advisory locking for safe multi-writer vault mutation.
#
# Closes the latent multi-writer corruption bug in v1.6 where two parallel
# sub-agents writing to the same wiki page could silently trample each other.
# The README and skills/wiki-ingest/SKILL.md §259-264 documented "single-writer
# only" as a convention; this script makes it an enforceable guard.
#
# Design (age-based, not flock-style):
# flock(2) advisory locks release when the holding process exits. That
# doesn't fit our model where `acquire` and `release` are SEPARATE bash
# invocations from the same skill (each Bash tool call is its own short-
# lived process — neither's PID survives long enough to mean anything).
# So we use atomic lockfile creation with `set -o noclobber` plus
# epoch-timestamp AGE-based staleness detection. Race-safe because the
# noclobber write itself is atomic on POSIX filesystems.
#
# The PID written into the lockfile is informational only (helpful for
# `list` and debugging). The acquire decision considers AGE only:
# - If lockfile age < STALE_AFTER_SEC → refuse (return 75 EX_TEMPFAIL)
# - If lockfile age >= STALE_AFTER_SEC → reap and acquire
# Default STALE_AFTER_SEC=60. Long enough for any single skill operation
# (page writes are milliseconds; a multi-write ingest pass is seconds);
# short enough that a crashed holder unblocks quickly.
#
# Semantics:
# acquire <vault-rel-path>
# - Computes lock_file = .vault-meta/locks/<sha1(path)>.lock
# - Atomically creates the lockfile with this process's PID + epoch
# - Returns 0 if acquired, 75 (EX_TEMPFAIL) if held and age < threshold
# - Auto-reaps locks older than STALE_AFTER_SEC
# release <vault-rel-path>
# - Removes the lockfile unconditionally (rm -f). Idempotent.
# - Cross-process release IS allowed by design — acquire and release
# are typically separate bash invocations from the same skill, and
# PID-matching would never succeed. Skill authors are trusted not to
# release locks they don't own; that's no weaker than `rm` on the
# lockfile directly.
# list
# - Prints currently-held lock records (one per line: pid age path).
# clear-stale [--max-age N]
# - Removes lockfiles whose PID is dead OR whose age > N seconds.
# Default N = 3600 (1h). Returns count removed via stdout.
# (The N=3600 default is intentionally generous because clear-stale
# is admin-grade cleanup, distinct from the per-acquire age threshold.)
# peek <vault-rel-path>
# - Prints holder info or "unheld"; exit 0; never mutates.
#
# Globals:
# STALE_AFTER_SEC — default 60. Override via --stale-after-sec N on any cmd.
#
# Age-threshold naming (v1.7.2; closes audit L6):
# - STALE_AFTER_SEC (default 60) is the PER-ACQUIRE threshold. A new
# acquire that finds an existing lock will reap-and-take if the lock is
# older than this; refuse otherwise. Tuned for "single skill operation
# completes within 60s."
# - `clear-stale --max-age N` (default 3600) is the ADMIN reaper threshold,
# meant to be run periodically by an operator or hook to sweep abandoned
# locks. Tuned for "anything older than an hour is definitely abandoned."
# These are two distinct concerns; both are time-since-acquire but operate
# at different scopes. Do not unify the defaults.
#
# Usage:
# bash scripts/wiki-lock.sh acquire wiki/concepts/Foo.md
# bash scripts/wiki-lock.sh release wiki/concepts/Foo.md
# bash scripts/wiki-lock.sh list
# bash scripts/wiki-lock.sh clear-stale --max-age 1800
# bash scripts/wiki-lock.sh peek wiki/concepts/Foo.md
#
# Exit codes:
# 0 — success
# 2 — usage error
# 75 — acquire failed (lock held by alive process)
# 3 — vault-meta/locks dir creation failed
# 4 — invalid vault-relative path (escape attempt)
set -euo pipefail
VAULT_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
META_DIR="${VAULT_ROOT}/.vault-meta"
LOCK_DIR="${META_DIR}/locks"
META_LOCK="${META_DIR}/.wiki-lock.meta"
STALE_AFTER_SEC=60
# ── helpers ──────────────────────────────────────────────────────────────────
die() { echo "ERR: $*" >&2; exit "${2:-2}"; }
log() { echo "$*" >&2; }
# Allow tests / non-default vault roots to override
if [ -n "${WIKI_LOCK_VAULT:-}" ]; then
VAULT_ROOT="$WIKI_LOCK_VAULT"
META_DIR="${VAULT_ROOT}/.vault-meta"
LOCK_DIR="${META_DIR}/locks"
META_LOCK="${META_DIR}/.wiki-lock.meta"
fi
sha1_of() {
if command -v sha1sum >/dev/null 2>&1; then
printf '%s' "$1" | sha1sum | awk '{print $1}'
else
# macOS fallback
printf '%s' "$1" | shasum -a 1 | awk '{print $1}'
fi
}
ensure_dirs() {
mkdir -p "$LOCK_DIR" 2>/dev/null || die "cannot create $LOCK_DIR" 3
}
validate_path() {
# Reject empty, absolute, escape, or newline-bearing paths to prevent
# lock-namespace pollution. v1.7.2 / closes audit M4: newlines would break
# the meta-lock line format (key=value lines separated by literal \n).
# v1.9.1 / closes audit M3 (symlink escape): when a vault-relative path
# resolves through a symlink to outside VAULT_ROOT, treat as path traversal.
local p="$1"
[ -z "$p" ] && die "path cannot be empty" 4
case "$p" in
/*) die "path must be vault-relative, not absolute: $p" 4 ;;
*..*) die "path may not contain '..': $p" 4 ;;
*$'\n'*) die "path may not contain newlines (lockfile format would break)" 4 ;;
*$'\r'*) die "path may not contain carriage returns" 4 ;;
esac
# Symlink canonicalization (only when the path or one of its parents exists).
# Non-existent paths can pass; the lock acquire itself creates leaves under
# LOCK_DIR, not the path itself. We resolve via python3 (portable across
# GNU coreutils + macOS BSD where realpath flag semantics differ).
if command -v python3 >/dev/null 2>&1; then
local resolved root
resolved=$(VAULT_ROOT_BASH="$VAULT_ROOT" P_BASH="$p" python3 -c '
import os, sys
root = os.path.realpath(os.environ["VAULT_ROOT_BASH"])
candidate = os.environ["P_BASH"]
target = os.path.realpath(os.path.join(root, candidate))
common = os.path.commonpath([root, target]) if target else ""
sys.stdout.write("INSIDE" if common == root else "OUTSIDE")
' 2>/dev/null)
[ "$resolved" = "OUTSIDE" ] && die "path resolves outside vault via symlink: $p" 4
fi
return 0
}
now_epoch() { date +%s; }
is_alive() {
# kill -0 returns 0 if process exists and we can signal it
kill -0 "$1" 2>/dev/null
}
# Atomic meta-lock wrapper. Funcs that mutate LOCK_DIR call under this lock so
# acquire/release/clear-stale don't race against each other.
with_meta_lock() {
ensure_dirs
# Use flock under bash's redirect; meta lock is short-lived per command.
(
flock -x -w 5 9 || die "could not acquire meta-lock within 5s" 1
"$@"
) 9>"$META_LOCK"
}
read_lockfile() {
# Echoes: <pid> <epoch> <path> (or empty if file missing/unreadable)
local lf="$1"
[ -f "$lf" ] || return 0
head -1 "$lf" 2>/dev/null || true
}
# ── commands ─────────────────────────────────────────────────────────────────
_cmd_acquire() {
local path="$1"
validate_path "$path"
ensure_dirs
local lf="${LOCK_DIR}/$(sha1_of "$path").lock"
local now
now=$(now_epoch)
# Try the cheap path first: noclobber-atomic create
if (set -o noclobber; printf '%s %s %s\n' "$$" "$now" "$path" > "$lf") 2>/dev/null; then
return 0
fi
# Lockfile already exists — examine age, not PID
local existing
existing=$(read_lockfile "$lf")
if [ -z "$existing" ]; then
# Empty/unreadable; treat as stale, clean and retry once
rm -f "$lf"
if (set -o noclobber; printf '%s %s %s\n' "$$" "$now" "$path" > "$lf") 2>/dev/null; then
return 0
fi
return 75
fi
local eepoch
eepoch=$(printf '%s' "$existing" | awk '{print $2}')
# Numeric sanity (corrupt lockfile → treat as stale)
case "$eepoch" in
''|*[!0-9]*) rm -f "$lf"
(set -o noclobber; printf '%s %s %s\n' "$$" "$now" "$path" > "$lf") 2>/dev/null && return 0
return 75 ;;
esac
local age=$((now - eepoch))
if [ "$age" -gt "$STALE_AFTER_SEC" ]; then
# Age exceeds threshold → reap and re-acquire (regardless of holder PID)
rm -f "$lf"
if (set -o noclobber; printf '%s %s %s\n' "$$" "$now" "$path" > "$lf") 2>/dev/null; then
return 0
fi
return 75
fi
# Held and not yet stale by age — refuse
return 75
}
_cmd_release() {
local path="$1"
validate_path "$path"
ensure_dirs
local lf="${LOCK_DIR}/$(sha1_of "$path").lock"
# Unconditional remove — cross-process release is allowed by design
# (acquire and release are typically separate bash invocations from the
# same skill; PID-matching would never succeed). See header comment.
rm -f "$lf"
return 0
}
_cmd_list() {
ensure_dirs
local count=0
for lf in "$LOCK_DIR"/*.lock; do
[ -f "$lf" ] || continue
local rec
rec=$(read_lockfile "$lf")
[ -n "$rec" ] || continue
local pid epoch path now age
pid=$(printf '%s' "$rec" | awk '{print $1}')
epoch=$(printf '%s' "$rec" | awk '{print $2}')
path=$(printf '%s' "$rec" | cut -d' ' -f3-)
now=$(now_epoch)
age=$((now - epoch))
printf 'pid=%s age=%ss path=%s\n' "$pid" "$age" "$path"
count=$((count + 1))
done
return 0
}
_cmd_clear_stale() {
local max_age="$1"
ensure_dirs
local removed=0
local now
now=$(now_epoch)
for lf in "$LOCK_DIR"/*.lock; do
[ -f "$lf" ] || continue
local rec
rec=$(read_lockfile "$lf")
if [ -z "$rec" ]; then
rm -f "$lf"; removed=$((removed + 1)); continue
fi
local pid epoch age
pid=$(printf '%s' "$rec" | awk '{print $1}')
epoch=$(printf '%s' "$rec" | awk '{print $2}')
age=$((now - epoch))
if ! is_alive "$pid" || [ "$age" -gt "$max_age" ]; then
rm -f "$lf"; removed=$((removed + 1))
fi
done
echo "$removed"
return 0
}
_cmd_peek() {
local path="$1"
validate_path "$path"
ensure_dirs
local lf="${LOCK_DIR}/$(sha1_of "$path").lock"
if [ ! -f "$lf" ]; then
echo "unheld"
return 0
fi
local rec
rec=$(read_lockfile "$lf")
echo "$rec"
return 0
}
# ── arg parsing (flags accepted in any position) ─────────────────────────────
if [ $# -lt 1 ]; then
sed -n '2,46p' "$0" | sed 's/^# \{0,1\}//'
exit 2
fi
CMD=""
ARGS=()
MAX_AGE_OVERRIDE=""
while [ $# -gt 0 ]; do
case "$1" in
--stale-after-sec) STALE_AFTER_SEC="$2"; shift 2 ;;
--max-age) MAX_AGE_OVERRIDE="$2"; shift 2 ;;
-h|--help) sed -n '2,46p' "$0" | sed 's/^# \{0,1\}//'; exit 0 ;;
--) shift; while [ $# -gt 0 ]; do ARGS+=("$1"); shift; done ;;
-*) die "unknown flag: $1" ;;
*)
if [ -z "$CMD" ]; then
CMD="$1"
else
ARGS+=("$1")
fi
shift
;;
esac
done
[ -n "$CMD" ] || die "no command given"
case "$CMD" in
acquire)
[ ${#ARGS[@]} -ge 1 ] || die "acquire needs a path"
with_meta_lock _cmd_acquire "${ARGS[0]}"
;;
release)
[ ${#ARGS[@]} -ge 1 ] || die "release needs a path"
with_meta_lock _cmd_release "${ARGS[0]}"
;;
list)
with_meta_lock _cmd_list
;;
clear-stale)
MAX="${MAX_AGE_OVERRIDE:-${ARGS[0]:-3600}}"
with_meta_lock _cmd_clear_stale "$MAX"
;;
peek)
[ ${#ARGS[@]} -ge 1 ] || die "peek needs a path"
with_meta_lock _cmd_peek "${ARGS[0]}"
;;
*)
die "unknown command: $CMD (try acquire|release|list|clear-stale|peek)"
;;
esac
scripts/wiki-mode.py
+252
View File
@@ -0,0 +1,252 @@
#!/usr/bin/env python3
"""wiki-mode.py — read + route helper for v1.8 methodology modes.
Single source of truth for "which mode is this vault in" and "where should
new content of type X be filed under mode Y." Consumed by:
- skills/wiki-ingest/SKILL.md (where to file new source/entity/concept pages)
- skills/save/SKILL.md (where to file session notes)
- skills/autoresearch/SKILL.md (where to file research output)
- bin/setup-mode.sh (writes .vault-meta/mode.json)
If `.vault-meta/mode.json` is absent → mode = "generic" → behavior identical
to v1.7. No skill needs to special-case the missing-config path.
CLI:
wiki-mode.py get # print current mode (default: generic)
wiki-mode.py config # print full config JSON
wiki-mode.py route TYPE NAME # print suggested path for new content
# TYPE: source|entity|concept|session|research
wiki-mode.py set MODE # write mode (lyt|para|zettelkasten|generic)
wiki-mode.py id # mint a Zettelkasten ID (timestamp)
wiki-mode.py templates # list per-mode template files
Exit codes:
0 — success
2 — usage error
3 — invalid mode string
4 — invalid content type
"""
import argparse
import json
import re
import sys
import tempfile
from datetime import datetime, timezone
from pathlib import Path
VAULT_ROOT = Path(__file__).resolve().parent.parent
META_DIR = VAULT_ROOT / ".vault-meta"
MODE_PATH = META_DIR / "mode.json"
VALID_MODES = ("generic", "lyt", "para", "zettelkasten")
VALID_TYPES = ("source", "entity", "concept", "session", "research")
DEFAULT_CONFIG = {
"schema_version": 1,
"mode": "generic",
"configured_at": None,
"config": {
"lyt": {
"moc_folder": "wiki/mocs/",
"notes_folder": "wiki/notes/",
},
"para": {
"projects_folder": "wiki/projects/",
"areas_folder": "wiki/areas/",
"resources_folder": "wiki/resources/",
"archives_folder": "wiki/archives/",
},
"zettelkasten": {
"id_format": "YYYYMMDDHHMMSSffffff",
"no_folders": True,
"root_folder": "wiki/",
},
"generic": {
"sources_folder": "wiki/sources/",
"entities_folder": "wiki/entities/",
"concepts_folder": "wiki/concepts/",
"sessions_folder": "wiki/sessions/",
},
},
}
def load_config():
"""Return parsed mode.json, or DEFAULT_CONFIG with mode='generic' if absent."""
if not MODE_PATH.is_file():
return dict(DEFAULT_CONFIG)
try:
loaded = json.loads(MODE_PATH.read_text(encoding="utf-8"))
# Merge with defaults so partially-configured files still work
merged = dict(DEFAULT_CONFIG)
merged["mode"] = loaded.get("mode", "generic")
merged["configured_at"] = loaded.get("configured_at")
loaded_config = loaded.get("config", {})
for k, v in loaded_config.items():
if k in merged["config"] and isinstance(v, dict):
merged["config"][k].update(v)
return merged
except (json.JSONDecodeError, OSError) as e:
print(f"ERR: cannot parse {MODE_PATH}: {e}", file=sys.stderr)
print(" Falling back to mode=generic. Re-run `bash bin/setup-mode.sh` to fix.",
file=sys.stderr)
return dict(DEFAULT_CONFIG)
def save_config(cfg):
META_DIR.mkdir(parents=True, exist_ok=True)
payload = json.dumps(cfg, indent=2, ensure_ascii=False) + "\n"
fd, tmp_path = tempfile.mkstemp(prefix="mode.", suffix=".tmp", dir=str(META_DIR))
try:
with open(fd, "w", encoding="utf-8") as fh:
fh.write(payload)
Path(tmp_path).replace(MODE_PATH)
except Exception:
try:
Path(tmp_path).unlink()
except OSError:
pass
raise
def slugify(name):
"""Filesystem-safe slug; matches the convention used by the existing skills.
Any run of non-word, non-hyphen characters becomes a single hyphen so that
'v1.8 launch! prep?' → 'v1-8-launch-prep' (not 'v18launchprep').
Unicode word characters (CJK, accented Latin, Cyrillic, etc.) are preserved.
"""
s = re.sub(r"[^\w\-]+", "-", name, flags=re.UNICODE)
s = re.sub(r"-+", "-", s).strip("-")
return s or "untitled"
def safe_name(name):
"""Sanitize a name that intentionally preserves case + spaces (entity/concept).
Strips path separators, null bytes, control characters, and leading dots or
hyphens so the returned string cannot escape its parent directory or be
interpreted as a hidden file or flag. Spaces and case are preserved.
"""
cleaned = re.sub(r"[/\\\x00-\x1f]+", "", name)
cleaned = cleaned.lstrip(".-")
return cleaned or "untitled"
def mint_zettel_id():
"""YYYYMMDDHHMMSSffffff in UTC (microsecond resolution).
Stable across timezones; lexicographically sortable; collision-resistant
against rapid back-to-back calls in the same second. Microsecond suffix
closes the v1.8.0 verifier LOW (two rapid mint calls produced the same
14-digit ID and would have generated colliding filenames).
"""
return datetime.now(timezone.utc).strftime("%Y%m%d%H%M%S%f")
def route_path(mode, content_type, name, cfg):
"""Return the suggested vault-relative path for new content under `mode`."""
if content_type not in VALID_TYPES:
raise SystemExit(4)
slug = slugify(name)
raw = safe_name(name) # case + spaces preserved, but path-traversal stripped
if mode == "generic":
g = cfg["config"]["generic"]
mapping = {
"source": g["sources_folder"] + slug + ".md",
"entity": g["entities_folder"] + raw + ".md", # preserve capitalization for entities
"concept": g["concepts_folder"] + raw + ".md",
"session": g["sessions_folder"] + slug + ".md",
"research": g["concepts_folder"] + raw + ".md",
}
return mapping[content_type]
if mode == "lyt":
notes = cfg["config"]["lyt"]["notes_folder"]
# All atomic notes flat in wiki/notes/; routing is the same regardless of type
return notes + slug + ".md"
if mode == "para":
p = cfg["config"]["para"]
mapping = {
# New sources land in resources/<topic>/ (we use a generic 'incoming' bucket;
# the user will sort into specific topics via their own workflow)
"source": p["resources_folder"] + "incoming/" + slug + ".md",
"entity": p["resources_folder"] + "people/" + raw + ".md",
"concept": p["resources_folder"] + "concepts/" + raw + ".md",
# Session notes land in projects/inbox/; user reroutes to specific projects
"session": p["projects_folder"] + "inbox/" + slug + ".md",
"research": p["resources_folder"] + slug + "/" + slug + ".md",
}
return mapping[content_type]
if mode == "zettelkasten":
z = cfg["config"]["zettelkasten"]
zid = mint_zettel_id()
return z["root_folder"] + f"{zid}-{slug}.md"
raise SystemExit(3)
def main():
parser = argparse.ArgumentParser(description="Methodology-mode router for v1.8 Compound Vault.")
sub = parser.add_subparsers(dest="cmd", required=True)
sub.add_parser("get", help="Print current mode")
sub.add_parser("config", help="Print full config JSON")
sp_route = sub.add_parser("route", help="Print suggested vault path for new content")
sp_route.add_argument("type", choices=VALID_TYPES)
sp_route.add_argument("name", help="Content name (will be slugified for filenames)")
sp_route.add_argument("--mode", choices=VALID_MODES, default=None,
help="Preview routing under MODE without writing mode.json (default: use current vault mode)")
sp_set = sub.add_parser("set", help="Write a mode to .vault-meta/mode.json")
sp_set.add_argument("mode", choices=VALID_MODES)
sub.add_parser("id", help="Mint a Zettelkasten ID (timestamp)")
sub.add_parser("templates", help="List per-mode template files")
args = parser.parse_args()
cfg = load_config()
if args.cmd == "get":
print(cfg["mode"])
return 0
if args.cmd == "config":
print(json.dumps(cfg, indent=2, ensure_ascii=False))
return 0
if args.cmd == "route":
active_mode = args.mode if args.mode else cfg["mode"]
path = route_path(active_mode, args.type, args.name, cfg)
print(path)
return 0
if args.cmd == "set":
cfg["mode"] = args.mode
cfg["configured_at"] = datetime.now(timezone.utc).strftime("%Y-%m-%dT%H:%M:%SZ")
save_config(cfg)
print(f"mode set: {args.mode}")
return 0
if args.cmd == "id":
print(mint_zettel_id())
return 0
if args.cmd == "templates":
templates_dir = VAULT_ROOT / "skills" / "wiki-mode" / "templates"
if not templates_dir.is_dir():
print(f"ERR: templates dir missing: {templates_dir}", file=sys.stderr)
return 2
for f in sorted(templates_dir.rglob("*.md")):
print(str(f.relative_to(VAULT_ROOT)))
return 0
return 2
if __name__ == "__main__":
sys.exit(main())
skills/autoresearch/SKILL.md
+298
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@@ -0,0 +1,298 @@
---
name: autoresearch
description: >
Autonomous iterative research loop. Takes a topic, runs web searches, fetches sources,
synthesizes findings, and files everything into the wiki as structured pages.
Based on Karpathy's autoresearch pattern: program.md configures objectives and constraints,
the loop runs until depth is reached, output goes directly into the knowledge base.
Triggers on: "/autoresearch", "autoresearch", "research [topic]", "deep dive into [topic]",
"investigate [topic]", "find everything about [topic]", "research and file",
"go research", "build a wiki on".
allowed-tools: Read Write Edit Glob Grep WebFetch WebSearch
---
# autoresearch: Autonomous Research Loop
You are a research agent. You take a topic, run iterative web searches, synthesize findings, and file everything into the wiki. The user gets wiki pages, not a chat response.
This is based on Karpathy's autoresearch pattern: a configurable program defines your objectives. You run the loop until depth is reached. Output goes into the knowledge base.
---
## Transport (v1.7+)
The research loop writes a lot — source pages, concept pages, entity pages, manifest updates. All writes follow the standard transport policy. Read `.vault-meta/transport.json` (auto-created by `bash scripts/detect-transport.sh`):
- **cli** — `obsidian-cli write "$VAULT" "$NOTE" < content.md`; see [`skills/wiki-cli/SKILL.md`](../wiki-cli/SKILL.md)
- **mcp-obsidian** / **mcpvault** — `mcp__obsidian-vault__write_note`
- **filesystem** — Claude's `Write` tool with absolute path
Full decision tree: [`wiki/references/transport-fallback.md`](../../wiki/references/transport-fallback.md). Web fetches (`WebFetch`/`WebSearch`) are transport-agnostic.
---
## Mode awareness (v1.8+)
Before filing research output, consult the vault's methodology mode via `python3 scripts/wiki-mode.py route research "<topic>"`. The router returns the vault-relative path:
- **generic**: `wiki/concepts/<Topic>.md` (v1.7 default)
- **LYT**: `wiki/notes/<topic>.md` + create or update a topic MOC at `wiki/mocs/<topic>-moc.md`
- **PARA**: `wiki/resources/<topic>/<topic>.md` (topic-named subfolder under resources)
- **Zettelkasten**: `wiki/<ID>-<topic>.md` (timestamped ID prefix)
If `.vault-meta/mode.json` is absent, the router returns mode=generic paths.
When the research session produces multiple entity / concept pages alongside the main synthesis, route EACH via the appropriate router call (`route entity` / `route concept`), not just the synthesis page. Mode awareness applies to every new file the loop creates.
## Web egress hygiene (v1.8.2+)
Autoresearch calls `WebFetch` and `WebSearch` to pull arbitrary URLs. Before each fetch and before writing fetched content to the vault, apply these guards:
**1. URL validation.** Reject these schemes and targets:
- `file://`, `javascript:`, `data:` schemes — fetch only `http(s)://`
- RFC1918 private addresses (`10.x.x.x`, `172.16-31.x.x`, `192.168.x.x`) and `localhost`/`127.0.0.1` — these would target the user's internal network
- Hosts not surfaced by the prior `WebSearch` step (be conservative; do not follow redirects to domains that never appeared in search results)
The Claude Code `WebFetch` tool has built-in defenses against many of these. Apply them here as defense-in-depth.
**2. Content sanitization before writing fetched HTML into a wiki page.** Fetched content can contain prompt-style injections, fake wikilinks, or executable code fences. Before any `Write` to `wiki/sources/<source>.md`:
- Strip `<script>`, `<iframe>`, `<style>` tags and their contents
- Escape `[[` and `]]` in the source body so adversarial content cannot inject wikilinks into the vault's link graph (encode as `\[\[` or HTML-entity `&#91;&#91;`)
- Reject any `---` YAML-frontmatter delimiter inside fetched content — the source page's frontmatter is authored by the loop, not by the upstream source
- Truncate fetched bodies to ~50KB to avoid context blowout
**3. Per-loop cost expectation.** A full autoresearch run is up to **3 rounds × 5 sources × 3 angles ≈ 45 `WebFetch` calls**. WebFetch is metered through the Anthropic plan. The `max_pages: 15` cap in `references/program.md` limits FILING cost but does NOT cap FETCH count. Surface the budget expectation to the user before kicking off research on a high-cost topic.
**4. Failure mode.** If a fetch fails (timeout, 4xx/5xx, content too large, sanitization removed everything), log the URL + reason to `wiki/log.md` and continue the loop. Do NOT abort the whole run. Do NOT silently swallow — every skipped source is a fact the user needs in the synthesis page's "Open Questions" section.
The router (`python3 scripts/wiki-mode.py route`) already sanitizes the topic-derived FILENAME via `safe_name()`. This section adds the second layer: BODY-content hygiene for fetched pages.
---
## Concurrency (v1.7+)
The research loop is a high write-rate skill (often 10-30 page writes per topic). Every wiki page write MUST be preceded by `wiki-lock acquire <path>`:
```bash
bash scripts/wiki-lock.sh acquire wiki/sources/<slug>.md || sleep 2 && bash scripts/wiki-lock.sh acquire wiki/sources/<slug>.md
# … write via §Transport-selected method …
bash scripts/wiki-lock.sh release wiki/sources/<slug>.md
```
If autoresearch is invoked in parallel (e.g., two `/autoresearch` commands fired at once on overlapping topics), the locks ensure that the same source/concept/entity page is written by only one loop at a time. The losing acquire skips that page for the current pass and logs `wiki/log.md`; the page will be picked up in the next iteration of the winning loop's pass.
See `skills/wiki-ingest/SKILL.md` §Concurrency for the full lock semantics.
---
## Before Starting
Read `references/program.md` to load the research objectives and constraints. This file is user-configurable. It defines what sources to prefer, how to score confidence, and any domain-specific constraints.
---
## Topic Selection
Three paths to a topic:
### A. Explicit topic (always respected)
When the user says `/autoresearch [topic]` or "research X", use the given topic verbatim and skip the sections below.
### B. Boundary-first selection (agenda control, opt-in)
**This is agenda control, not pure memory.** DragonScale Memory.md Mechanism 4 labels this mechanism as such because it shapes which direction the research agent moves next. Users who want a strict memory-layer subset should omit this path entirely.
When `/autoresearch` is invoked WITHOUT a topic AND the vault has adopted DragonScale, default to surfacing the frontier of the vault as a set of candidate topics the user can accept, override, or decline.
Feature detection (shell):
```bash
if [ -x ./scripts/boundary-score.py ] && [ -d ./.vault-meta ] && command -v python3 >/dev/null 2>&1; then
BOUNDARY_MODE=1
else
BOUNDARY_MODE=0
fi
```
When `BOUNDARY_MODE=1`:
1. Run `./scripts/boundary-score.py --json --top 5`. Returns the top 5 frontier pages by `boundary_score = (out_degree - in_degree) * recency_weight`.
2. **Helper failure handling**: if the helper exits non-zero, emits invalid JSON, or returns an empty `results` array, set `BOUNDARY_MODE=0` and fall through to section C below. Do NOT prompt the user with an empty candidate list, and do NOT improvise a topic.
3. Present the candidate list to the user: "Your top frontier pages are: [list]. Research which one? (1-5, or type a topic to override, or say 'cancel' to be asked normally.)"
4. If the user picks 1-5, use the selected page's title as the topic.
5. If the user types free text, use that.
6. If the user cancels or does not choose, fall through to C.
The boundary score is a heuristic, not an objective measure of what SHOULD be researched. The user always has the option to type a free-text topic to override the surfaced candidates.
**Link-resolution semantics**: the boundary helper uses **filename-stem wikilink resolution only**. `[[Foo]]` is counted as an edge to `Foo.md` anywhere in the vault. Aliases declared via frontmatter `aliases:` are **not** parsed. Folder-qualified links (e.g. `[[notes/Foo]]`) are resolved by stem only. This matches default Obsidian behavior for unique filenames but does not implement full Obsidian alias resolution.
### C. User-chosen (default when B is unavailable)
When `BOUNDARY_MODE=0` or the user declined every frontier pick, ask: "What topic should I research?"
---
## Research Loop
```
Input: topic (from Topic Selection, above)
Round 1. Broad search
1. Decompose topic into 3-5 distinct search angles
2. For each angle: run 2-3 WebSearch queries
3. For top 2-3 results per angle: WebFetch the page
4. Extract from each: key claims, entities, concepts, open questions
Round 2. Gap fill
5. Identify what's missing or contradicted from Round 1
6. Run targeted searches for each gap (max 5 queries)
7. Fetch top results for each gap
Round 3. Synthesis check (optional, if gaps remain)
8. If major contradictions or missing pieces still exist: one more targeted pass
9. Otherwise: proceed to filing
Max rounds: 3 (as set in program.md). Stop when depth is reached or max rounds hit.
```
---
## Filing Results
After research is complete, create these pages:
**wiki/sources/**. One page per major reference found
- Use source frontmatter (type, source_type, author, date_published, url, confidence, key_claims)
- Body: summary of the source, what it contributes to the topic
**wiki/concepts/**. One page per significant concept extracted
- Only create a page if the concept is substantive enough to stand alone
- Check the index first: update existing concept pages rather than creating duplicates
**wiki/entities/**. One page per significant person, org, or product identified
- Check the index first: update existing entity pages
**wiki/questions/**. One synthesis page titled "Research: [Topic]"
- This is the master synthesis. Everything comes together here.
- Sections: Overview, Key Findings, Entities, Concepts, Contradictions, Open Questions, Sources
- Full frontmatter with related links to all pages created in this session
---
## Synthesis Page Structure
```markdown
---
type: synthesis
title: "Research: [Topic]"
created: YYYY-MM-DD
updated: YYYY-MM-DD
tags:
- research
- [topic-tag]
status: developing
related:
- "[[Every page created in this session]]"
sources:
- "[[wiki/sources/Source 1]]"
- "[[wiki/sources/Source 2]]"
---
# Research: [Topic]
## Overview
[2-3 sentence summary of what was found]
## Key Findings
- Finding 1 (Source: [[Source Page]])
- Finding 2 (Source: [[Source Page]])
- ...
## Key Entities
- [[Entity Name]]: role/significance
## Key Concepts
- [[Concept Name]]: one-line definition
## Contradictions
- [[Source A]] says X. [[Source B]] says Y. [Brief note on which is more credible and why]
## Open Questions
- [Question that research didn't fully answer]
- [Gap that needs more sources]
## Sources
- [[Source 1]]: author, date
- [[Source 2]]: author, date
```
---
## After Filing
1. Update `wiki/index.md`. Add all new pages to the right sections
2. Append to `wiki/log.md` (at the TOP):
```
## [YYYY-MM-DD] autoresearch | [Topic]
- Rounds: N
- Sources found: N
- Pages created: [[Page 1]], [[Page 2]], ...
- Synthesis: [[Research: Topic]]
- Key finding: [one sentence]
```
3. Update `wiki/hot.md` with the research summary
---
## Report to User
After filing everything:
```
Research complete: [Topic]
Rounds: N | Searches: N | Pages created: N
Created:
wiki/questions/Research: [Topic].md (synthesis)
wiki/sources/[Source 1].md
wiki/concepts/[Concept 1].md
wiki/entities/[Entity 1].md
Key findings:
- [Finding 1]
- [Finding 2]
- [Finding 3]
Open questions filed: N
```
---
## Constraints
Follow the limits in `references/program.md`:
- Max rounds (default: 3)
- Max pages per session (default: 15)
- Confidence scoring rules
- Source preference rules
If a constraint conflicts with completeness, respect the constraint and note what was left out in the Open Questions section.
---
## How to think (10-principle mapping)
When working on this skill, apply the 10-principle loop. See [`skills/think/SKILL.md`](../think/SKILL.md) for the canonical framework.
| # | Principle | Application here |
|---|-----------|-------------------|
| 1 | OBSERVE (ext) | Read `references/program.md` to load constraints. Read the topic verbatim. Note what's already in the wiki. |
| 2 | OBSERVE (int) | Am I steering the search toward what I already expect to find? Confirmation bias kills research. |
| 3 | LISTEN | The user's framing + cultural context + the counter-position the user might NOT have considered. |
| 4 | THINK | 3-5 distinct search angles that cover the topic without overlap; credibility-weighted source filter. |
| 5 | CONNECT (lat) | Cross-source corroboration vs contradiction — the synthesis lives at the intersection, not in any single source. |
| 6 | CONNECT (sys) | WebFetch + WebSearch + §Web egress hygiene + wiki-mode router + wiki-lock for multi-writer safety. |
| 7 | FEEL | 30 pages of low-signal noise wastes the user's time and Anthropic plan budget. Quality over volume. |
| 8 | ACCEPT | Missing sources are part of the synthesis — file them under Open Questions, don't paper over. |
| 9 | CREATE | Synthesis page + sources + entities + concepts; full traceability per claim. |
| 10 | GROW | Open Questions feed the next research cycle; the loop is incremental, not exhaustive. |
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# Research Program
This file configures the autoresearch loop. Edit it to match your domain and research style. The autoresearch skill reads it before every run.
---
## Search Objectives
Default objectives for every research session:
- Find authoritative sources (prefer: .edu, peer-reviewed papers, official documentation, primary sources, established publications)
- Extract key entities (people, organizations, products, tools)
- Extract key concepts and frameworks
- Note contradictions between sources
- Identify open questions and research gaps
- Prefer sources from the last 2 years unless the topic is foundational
---
## Confidence Scoring
Label every claim with confidence when filing:
- **high**: multiple independent authoritative sources agree
- **medium**: single good source, or sources partially agree
- **low**: speculation, opinion pieces, single informal source, or claim not verified
Always note the source date for factual claims. Mark claims from sources older than 3 years as potentially stale.
---
## Loop Constraints
- Max search rounds per topic: **3**
- Max wiki pages created per session: **15**
- Max sources fetched per round: **5**
- If max pages is reached before the loop completes: file what you have, note what was skipped in Open Questions
---
## Output Style
- Declarative, present tense
- Cite every non-obvious claim: `(Source: [[Page]])`
- Short pages: under 200 lines. Split if longer.
- No hedging language ("it seems", "perhaps", "might be")
- Flag uncertainty explicitly: `> [!gap] This claim needs verification.`
---
## Domain Notes
[Add domain-specific instructions here. Examples:]
For AI/tech research:
- Prefer: arXiv, official GitHub repos, official product documentation, Hacker News discussions with high karma
- Note: LLM benchmarks are often gamed: treat leaderboard claims as low confidence unless independently verified
For business/market research:
- Prefer: company filings, Crunchbase, Bloomberg, verified industry reports
- Flag: press releases as low confidence without independent verification
For medical/health research:
- Prefer: PubMed, Cochrane reviews, peer-reviewed clinical trials
- Always note: sample size, study type (RCT vs observational), and recency
---
## Exclusions
Do not cite as high-confidence sources:
- Reddit posts or forums (use as pointers to primary sources only)
- Social media posts
- Undated web pages
- Sources that don't cite their own claims
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---
name: canvas
description: "Visual layer of the wiki. Add images, text cards, PDFs, and wiki pages to Obsidian canvas files with auto-positioning inside zones. Integrates with /banana for image capture. Triggers on: /canvas, canvas new, canvas add image, canvas add text, canvas add pdf, canvas add note, canvas zone, canvas list, canvas from banana, add to canvas, put this on the canvas, open canvas, create canvas."
allowed-tools: Read Write Edit Glob Grep
---
# canvas: Visual Reference Layer
The three knowledge capture layers:
- `/save` → text synthesis (wiki/questions/, wiki/concepts/)
- `/autoresearch` → structured knowledge (wiki/sources/, wiki/concepts/)
- `/canvas` → visual references (wiki/canvases/)
A canvas is a JSON file Obsidian renders as an infinite visual board. This skill reads and writes canvas JSON directly. Read `references/canvas-spec.md` for the full format reference before making any edits. This spec aligns with the [JSON Canvas open standard](https://jsoncanvas.org/).
**Substrate preference (v1.7+)**: This skill is a self-contained fallback. **Prefer `kepano/obsidian-skills`** as the authoritative substrate — its `json-canvas` skill is the canonical spec reference. If you see a `json-canvas` skill available without the `claude-obsidian:` namespace, that is kepano's version: use it for spec questions. Continue to use this `canvas` skill for the wiki-scoped *workflows* (positioning into wiki/canvases/, /banana integration, zone layout) — those are unique to claude-obsidian and live above kepano's primitive. Install kepano: `claude plugin marketplace add kepano/obsidian-skills`.
---
## Default Canvas
`wiki/canvases/main.canvas`
If it does not exist, create it:
```json
{
"nodes": [
{
"id": "title",
"type": "text",
"text": "# Visual Reference\n\nDrop images, PDFs, and notes here.",
"x": -400, "y": -300, "width": 400, "height": 120, "color": "6"
},
{
"id": "zone-default",
"type": "group",
"label": "General",
"x": -400, "y": -140, "width": 800, "height": 400, "color": "4"
}
],
"edges": []
}
```
---
## Operations
### open / status (`/canvas` with no args)
1. Check if `wiki/canvases/main.canvas` exists.
2. If yes: read it, count nodes by type, list all group node labels (zone names).
Report: "Canvas has N nodes: X images, Y text cards, Z wiki pages. Zones: [list]"
3. If no: create it with the starter structure above.
Report: "Created main.canvas with a General zone."
4. Tell user: "Open `wiki/canvases/main.canvas` in Obsidian to view."
---
### new (`/canvas new [name]`)
1. Slugify the name: lowercase, spaces → hyphens, strip special chars.
2. Create `wiki/canvases/[slug].canvas` with the starter structure, title updated to `# [Name]`.
3. Add entry to `wiki/overview.md` under a "## Canvases" subsection (append after the Current State section). Do not modify `wiki/index.md`. It uses a fixed section schema (Domains, Entities, Concepts, Sources, Questions, Comparisons).
4. Report: "Created wiki/canvases/[slug].canvas"
---
### add image (`/canvas add image [path or url]`)
**Resolve the image:**
- If URL (starts with `http`): download with `curl -sL [url] -o _attachments/images/canvas/[filename]`
Derive filename from URL path, or use `img-[timestamp].jpg` if unclear.
- If local path outside vault: `cp [path] _attachments/images/canvas/`
- If already vault-relative: use as-is.
Create `_attachments/images/canvas/` if it doesn't exist.
**Detect aspect ratio:**
Use `python3 -c "from PIL import Image; img=Image.open('[path]'); print(img.width, img.height)"` or `identify -format '%w %h' [path]`.
See `references/canvas-spec.md` for the full aspect ratio → canvas size table (7 ratios including 4:3, 3:4, ultra-wide). Do not use an inline table here. The spec is the single source of truth for sizing.
**Position using auto-layout** (see Auto-Positioning section below).
**Append node to canvas JSON and write.**
Report: "Added [filename] to [zone] zone at position ([x], [y])."
---
### add text (`/canvas add text [content]`)
Create a text node:
```json
{
"id": "text-[timestamp]",
"type": "text",
"text": "[content]",
"x": [auto], "y": [auto],
"width": 300, "height": 120,
"color": "4"
}
```
Position using auto-layout. Write and report.
---
### add pdf (`/canvas add pdf [path]`)
Same as add image. Obsidian renders PDFs natively as file nodes.
- Copy to `_attachments/pdfs/canvas/` if outside vault.
- Fixed size: width=400, height=520.
- Report page count if you can determine it.
---
### add note (`/canvas add note [wiki-page]`)
1. Search `wiki/` for a file matching the page name (case-insensitive, partial match ok).
2. Use the vault-relative path as the `file` field.
- Use `"type": "file"` (not `"type": "link"`): `.md` files use file nodes, not link nodes.
- `"type": "link"` takes a `url: "https://..."`: it is for web URLs only.
3. Create a file node: width=300, height=100.
4. Position using auto-layout.
```json
{
"id": "note-[timestamp]",
"type": "file",
"file": "wiki/concepts/LLM Wiki Pattern.md",
"x": [auto], "y": [auto],
"width": 300, "height": 100
}
```
---
### zone (`/canvas zone [name] [color]`)
1. Read canvas JSON.
2. Find max_y: `max(node.y + node.height for all nodes) + 60`. Use 280 if no nodes (leaves room above the starter title node).
3. Create a group node:
```json
{
"id": "zone-[slug]",
"type": "group",
"label": "[name]",
"x": -400,
"y": [max_y],
"width": 1000,
"height": 400,
"color": "[color or '3']"
}
```
Valid colors: `"1"`=red `"2"`=orange `"3"`=yellow `"4"`=green `"5"`=cyan `"6"`=purple
Write and report.
---
### list (`/canvas list`)
1. `glob wiki/canvases/*.canvas`
2. For each canvas: read JSON, count nodes by type.
3. Report:
```
wiki/canvases/main.canvas . 14 nodes (8 images, 3 text, 2 file, 1 group)
wiki/canvases/design-ideas.canvas. 42 nodes (30 images, 4 text, 8 groups)
```
---
### from banana (`/canvas from banana`) (if the banana-claude plugin is installed)
1. Check `wiki/canvases/.recent-images.txt` first (session log of newly written images).
2. If not found or empty: use `find` with correct precedence (parentheses required. Without them `-newer` only binds to the last `-name` clause):
```bash
python3 -c "import time,os; open('/tmp/ten-min-ago','w').close(); os.utime('/tmp/ten-min-ago',(time.time()-600,time.time()-600))"
find _attachments/images -newer /tmp/ten-min-ago \( -name "*.png" -o -name "*.jpg" \)
```
Note: `/banana` is an optional external skill not shipped in this plugin. If the user has it installed, the `.recent-images.txt` log will be populated. If not, the `find` command above is the fallback.
3. If still none: show the 5 most recently modified images.
4. Present list: "Found N recent images: [list]. Add to canvas? Which zone? (zone name / 'new [name]' / 'skip')"
5. On confirmation: add each using the add image logic.
---
## Auto-Positioning Algorithm
Read `references/canvas-spec.md` for the full coordinate system.
```python
def next_position(canvas_nodes, target_zone_label, new_w, new_h):
# Find zone group node
zone = next((n for n in canvas_nodes
if n.get('type') == 'group'
and n.get('label') == target_zone_label), None)
if zone is None:
# No zone: place below all content
max_y = max((n['y'] + n.get('height', 0) for n in canvas_nodes), default=-140)
return -400, max_y + 60
zx, zy = zone['x'], zone['y']
zw, zh = zone['width'], zone['height']
# Nodes inside this zone
inside = [n for n in canvas_nodes
if n.get('type') != 'group'
and zx <= n['x'] < zx + zw
and zy <= n['y'] < zy + zh]
if not inside:
return zx + 20, zy + 20
rightmost_x = max(n['x'] + n.get('width', 0) for n in inside)
next_x = rightmost_x + 40
if next_x + new_w > zx + zw:
# New row
max_row_y = max(n['y'] + n.get('height', 0) for n in inside)
return zx + 20, max_row_y + 20
# Same row: align to the top of all existing nodes in the zone
current_row_y = min(n['y'] for n in inside)
return next_x, current_row_y
```
---
## ID Generation
Read the canvas, collect all existing IDs. Never reuse one.
Safe ID pattern: `[type]-[content-slug]-[full-unix-timestamp]`
Use the full Unix timestamp (10 digits) to avoid collisions in batch operations.
Examples: `img-cover-1744032823`, `text-note-1744032845`, `zone-branding-1744032901`
If a collision is detected (ID already exists in the canvas), append `-2`, `-3`, etc.
---
## Session Log (optional hook)
If `wiki/canvases/.recent-images.txt` exists, append any new image path written to `_attachments/images/` during this session (one path per line, keep last 20).
`/canvas from banana` reads this file first, making it instant without filesystem search.
---
## Banana Integration (if the banana-claude plugin is installed)
After any `/banana` run in the same session, if the user says "add to canvas" or "put on canvas", treat it as `/canvas from banana`.
When `/banana` finishes generating images, suggest:
> "Add generated images to canvas? Run `/canvas from banana`"
---
## Summary
1. Read canvas-spec.md before editing any canvas JSON.
2. Always read the canvas file before writing. Parse existing nodes to avoid ID collisions and calculate auto-positions.
3. Create `_attachments/images/canvas/` for downloaded/copied images.
4. Update `wiki/index.md` when creating new canvases.
5. Report position and zone after every add operation.
## See Also
For standalone visual production (12 templates, 6 layout algorithms, AI generation,
presentations), see [claude-canvas](https://github.com/AgriciDaniel/claude-canvas).
This skill handles wiki-scoped visual boards. claude-canvas handles full-featured
canvas orchestration for any project.
---
## How to think (10-principle mapping)
When working on this skill, apply the 10-principle loop. See [`skills/think/SKILL.md`](../think/SKILL.md) for the canonical framework.
| # | Principle | Application here |
|---|-----------|-------------------|
| 1 | OBSERVE (ext) | Which images, PDFs, notes belong on this canvas? Read each before adding. |
| 2 | OBSERVE (int) | Am I aestheticizing or actually communicating? Pretty canvases that don't inform are noise. |
| 3 | LISTEN | The user's mental model of how these items relate. The canvas should mirror that, not impose another. |
| 4 | THINK | Layout, group hierarchy, edge structure. Spatial reasoning matters; arbitrary positions confuse. |
| 5 | CONNECT (lat) | Edges between canvas nodes reveal hidden structure not visible in the linear wiki. |
| 6 | CONNECT (sys) | JSON Canvas 1.0 spec + Obsidian-native rendering + banana skill for AI image gen. |
| 7 | FEEL | A canvas should be readable at first glance, not a maze of arrows. |
| 8 | ACCEPT | Not every project needs a canvas. Admit when prose is enough. |
| 9 | CREATE | Write the `.canvas` JSON with stable IDs and sensible positions. |
| 10 | GROW | Which canvases get reopened? Which are abandoned? That signal informs canvas-worthiness over time. |
skills/canvas/references/canvas-spec.md
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# Obsidian Canvas JSON Specification
Canvas files are JSON with two top-level keys: `nodes` (array) and `edges` (array).
Obsidian reads and writes them as UTF-8 JSON files with `.canvas` extension.
This reference aligns with the [JSON Canvas 1.0 open specification](https://jsoncanvas.org/spec/1.0/). All structures support arbitrary additional fields (`[key: string]: any`) for forward compatibility. Obsidian will preserve unknown fields when reading and writing canvas files.
**ID format**: The JSON Canvas 1.0 spec recommends 16-character lowercase hexadecimal IDs (e.g., `"a1b2c3d4e5f67890"`). Obsidian itself generates IDs in this format. The descriptive ID examples in this reference (`"text-title-4821"`, `"img-cover-7823"`) are an alternative naming convention that this plugin uses for human readability. Both are valid JSON Canvas. Use whichever fits your workflow.
---
## Coordinate System
```
x increases →
┌─────────────────────────────────
│ (-920, -2400) (0, -2400)
│
y │ (-920, 0) (0, 0) ← origin
↓ │
│ (-920, 540) (500, 540)
```
- **Origin** (0, 0) is the center of the canvas viewport.
- **x increases rightward.** Negative x = left of center.
- **y increases downward.** Negative y = above center.
- Node `x` and `y` are the **top-left corner** of the node, not the center.
- Obsidian pans to fit all nodes on first open.
---
## Node Types
### Text node
Renders markdown content as a styled card.
```json
{
"id": "text-title-4821",
"type": "text",
"text": "# Heading\n\nParagraph with **bold** and `code`.",
"x": -400,
"y": -300,
"width": 400,
"height": 120,
"color": "6"
}
```
- `text`: markdown string. Use `\n` for newlines.
- Minimum readable size: width ≥ 200, height ≥ 60.
- `color` is optional. Omit for default (no color).
---
### File node
Renders an image, PDF, markdown note, or other vault file inline.
```json
{
"id": "img-cover-7823",
"type": "file",
"file": "_attachments/images/example.png",
"x": -900,
"y": -100,
"width": 420,
"height": 236
}
```
- `file`: **vault-relative path** (not absolute, not `~/`).
- Supported: `.png` `.jpg` `.webp` `.gif` `.pdf` `.md` `.canvas`
- For `.md` files: renders as a preview card.
- For `.pdf` files: renders the first page as preview.
- No `color` field for file nodes: color is ignored.
---
### Group node (Zone)
A labeled rectangular region. Does not clip or contain nodes. It's a visual guide.
Nodes placed "inside" a group are just positioned within its bounding box.
```json
{
"id": "zone-branding-3391",
"type": "group",
"label": "Brand Identity",
"x": -920,
"y": -880,
"width": 1060,
"height": 290,
"color": "6",
"background": "_attachments/images/grid-bg.png",
"backgroundStyle": "cover"
}
```
- `label`: shown at the top of the group box.
- `color`: colors the group border and label.
- `background` *(optional)*: vault-relative path to a background image for the group.
- `backgroundStyle` *(optional)*: how the background is rendered.
- `"cover"`: fills the group, cropping if needed (default-ish behavior)
- `"ratio"`: preserves aspect ratio, fits inside the group
- `"repeat"`: tiles the image
- Groups do not affect auto-layout: they are purely visual containers.
---
### Link node
Renders a web URL as an embedded preview card.
```json
{
"id": "link-karpathy-2233",
"type": "link",
"url": "https://github.com/karpathy",
"x": 200,
"y": -300,
"width": 400,
"height": 120
}
```
- `url`: must be a valid `https://` URL.
- Obsidian fetches the Open Graph preview (title, description, thumbnail).
---
## Edges
Connections between nodes. Usually empty for mood boards.
```json
{
"id": "e-hub-cidx",
"fromNode": "hub",
"fromSide": "right",
"fromEnd": "none",
"toNode": "c-idx",
"toSide": "left",
"toEnd": "arrow",
"label": "concepts",
"color": "5"
}
```
**Required fields**: `id`, `fromNode`, `toNode`. Everything else is optional.
- `fromNode` / `toNode`: IDs of the source and target nodes.
- `fromSide` / `toSide` *(optional)*: `"top"` `"bottom"` `"left"` `"right"`. If omitted, Obsidian auto-calculates the best side based on relative node positions.
- `fromEnd` *(optional)*: end-cap on the source side. Defaults to `"none"`. Values: `"none"` | `"arrow"`.
- `toEnd` *(optional)*: end-cap on the target side. **Defaults to `"arrow"`**: note the asymmetric default vs `fromEnd`. Values: `"none"` | `"arrow"`.
- `label` *(optional)*: text shown on the edge.
- `color` *(optional)*: same color palette as nodes (`"1"`–`"6"` or hex).
Most edges represent directed relationships, so the asymmetric defaults (`fromEnd: "none"`, `toEnd: "arrow"`) produce a single arrow pointing from source to target without specifying anything explicitly.
---
## Color Reference
| Code | Color | Hex (approx) | Use case |
|------|-------|-------------|----------|
| `"1"` | Red / Tomato | #e03e3e | Warnings, archive |
| `"2"` | Orange | #d09035 | Active work |
| `"3"` | Yellow / Gold | #d0a023 | WIP, notes |
| `"4"` | Green / Teal | #448361 | Content, sources |
| `"5"` | Blue / Cyan | #3ea7d3 | Navigation, info |
| `"6"` | Purple / Violet | #9063d2 | Title, identity |
Omit `color` entirely for the default (no border color, transparent label).
---
## Image Sizing Guidelines
Calculate from actual image dimensions using PIL or `identify`:
```bash
python3 -c "from PIL import Image; img=Image.open('path.png'); print(img.width, img.height)"
# or
identify -format '%w %h' path.png
```
| Aspect ratio | Condition | Canvas width | Canvas height |
|-------------|-----------|-------------|--------------|
| 16:9 (wide) | ratio 1.6–2.0 | 420 | 236 |
| 2:1 (ultra wide) | ratio > 2.0 | 440 | 220 |
| 4:3 | ratio 1.2–1.6 | 380 | 285 |
| 1:1 (square) | ratio 0.9–1.1 | 280 | 280 |
| 3:4 | ratio 0.6–0.9 | 240 | 320 |
| 9:16 (portrait) | ratio < 0.6 | 200 | 356 |
| PDF | any | 400 | 520 |
| Unknown | fallback | 320 | 240 |
---
## Auto-Positioning Pseudocode
```
function place_node(canvas, zone_label, new_w, new_h):
zone = find group node where label == zone_label
padding = 20
if zone not found:
max_y = max(n.y + n.height for n in canvas.nodes) + 60
return (-400, max_y)
# Nodes visually inside zone
inside = [n for n in canvas.nodes
if n.type != 'group'
and zone.x <= n.x < zone.x + zone.width
and zone.y <= n.y < zone.y + zone.height]
if inside is empty:
return (zone.x + padding, zone.y + padding)
# Rightmost point in zone
rightmost = max(n.x + n.width for n in inside)
next_x = rightmost + 40
if next_x + new_w > zone.x + zone.width - padding:
# Overflow → new row
bottom_of_row = max(n.y + n.height for n in inside)
return (zone.x + padding, bottom_of_row + padding)
# Same row
row_y = min(n.y for n in inside) # align to top of existing row
return (next_x, row_y)
```
---
## Full Example: Two-Zone Canvas
```json
{
"nodes": [
{
"id": "title-0001",
"type": "text",
"text": "# Brand Reference\n\n**AI Marketing Hub** visual assets",
"x": -920, "y": -2440, "width": 560, "height": 180, "color": "6"
},
{
"id": "zone-logos",
"type": "group",
"label": "Logos & Icons",
"x": -920, "y": -2200, "width": 1800, "height": 320, "color": "6"
},
{
"id": "img-logo-pro",
"type": "file",
"file": "_attachments/images/example.png",
"x": -900, "y": -2180, "width": 420, "height": 236
},
{
"id": "img-icon-free",
"type": "file",
"file": "_attachments/images/example-icon.png",
"x": -440, "y": -2180, "width": 280, "height": 280
},
{
"id": "zone-covers",
"type": "group",
"label": "Skill Covers",
"x": -920, "y": -1820, "width": 1800, "height": 340, "color": "3"
},
{
"id": "img-seo",
"type": "file",
"file": "_attachments/images/example-cover.png",
"x": -900, "y": -1800, "width": 420, "height": 236
}
],
"edges": []
}
```
---
## Common Mistakes
- **Wrong path format**: use `_attachments/images/file.png` not `/home/user/...` or `~/...`
- **ID collision**: always read existing IDs before generating a new one
- **Negative y confusion**: `y: -2400` is ABOVE `y: -1000` (more negative = higher up)
- **Group does not clip**: placing a node "inside" a group is just positioning it within the group's bounding box: there is no parent-child relationship in the JSON
- **Missing height on text nodes**: Obsidian will render the text but may clip it if height is too small. Use height ≥ content-lines × 24.
skills/defuddle/SKILL.md
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---
name: defuddle
description: "Strip clutter from web pages before ingesting into the wiki. Removes ads, navigation, headers, footers, and boilerplate: leaving clean readable markdown that saves 40-60% tokens. Triggers on: defuddle, clean this page, strip this url, fetch and clean, clean web content before ingesting, strip ads, remove clutter, clean URL content, readable markdown from URL."
allowed-tools: Read Bash
---
# defuddle: Web Page Cleaner
Defuddle extracts the meaningful content from a web page and drops everything else: ads, cookie banners, nav bars, related articles, footers, social sharing buttons. What remains is the article body as clean markdown.
Use this before any URL ingestion. It is optional but strongly recommended. It cuts token usage by 40-60% on typical web articles and produces cleaner wiki pages.
**Substrate note (v1.7+)**: Unlike `obsidian-markdown` / `obsidian-bases` / `json-canvas` (where we defer to kepano/obsidian-skills as upstream), the `defuddle` skill is original to claude-obsidian — kepano's marketplace does not ship a defuddle skill. This is the canonical version. The underlying `defuddle-cli` is independent of either marketplace and lives at [github.com/kepano/defuddle](https://github.com/kepano/defuddle).
---
## Install
```bash
npm install -g defuddle-cli
```
Verify: `defuddle --version`
---
## Usage
### Clean a URL directly
```bash
defuddle https://example.com/article
```
Outputs clean markdown to stdout.
### Save to .raw/
```bash
defuddle https://example.com/article > .raw/articles/article-slug-$(date +%Y-%m-%d).md
```
### Add frontmatter header after saving
After running defuddle, prepend the source URL and fetch date:
```bash
SLUG="article-slug-$(date +%Y-%m-%d)"
{ echo "---"; echo "source_url: https://example.com/article"; echo "fetched: $(date +%Y-%m-%d)"; echo "---"; echo ""; defuddle https://example.com/article; } > .raw/articles/$SLUG.md
```
### Clean a local HTML file
```bash
defuddle page.html
```
---
## When to Use
**Use defuddle when:**
- Ingesting a news article, blog post, or documentation page from a URL
- The page has a lot of surrounding content (most web pages do)
- You want to stay within token budget on a long article
**Skip defuddle when:**
- The source is already a clean markdown or PDF file
- The page is a dashboard, app, or structured data (defuddle expects article-style content)
- defuddle is not installed and the article is short enough to process raw
---
## Fallback
If defuddle is not installed, check:
```bash
which defuddle 2>/dev/null || echo "not installed"
```
If not installed: use WebFetch directly. The content will be less clean but still workable.
---
## Integration with /wiki-ingest
The `/wiki-ingest` skill checks for defuddle automatically when a URL is passed. You do not need to run defuddle manually before ingesting a URL. The ingest skill will call it if available.
To manually clean a page and save before ingesting:
1. Run the save command above
2. Then: `ingest .raw/articles/[slug].md`
---
## How to think (10-principle mapping)
When working on this skill, apply the 10-principle loop. See [`skills/think/SKILL.md`](../think/SKILL.md) for the canonical framework.
| # | Principle | Application here |
|---|-----------|-------------------|
| 1 | OBSERVE (ext) | Which URL? What's actually on the page? Don't assume the title matches the content. |
| 2 | OBSERVE (int) | Am I assuming the page has the content the user expects? Verify before extracting. |
| 3 | LISTEN | Did the user say "the article" (main content only) or "the link" (everything visible)? |
| 4 | THINK | Strip boilerplate, preserve structure, capture metadata. Quote URLs in shell to avoid injection. |
| 5 | CONNECT (lat) | How does this domain typically render? Some sites mangle defuddle's heuristics; track those. |
| 6 | CONNECT (sys) | Shells out to defuddle-cli (kepano); output lands in `.raw/` for wiki-ingest pickup. |
| 7 | FEEL | Clean markdown that reads like the original, not boilerplate residue. |
| 8 | ACCEPT | Some pages don't extract well. Flag and move on; don't force when the heuristic loses. |
| 9 | CREATE | Markdown to stdout, redirected to `.raw/articles/<slug>-<date>.md`. |
| 10 | GROW | Extraction failures suggest defuddle-cli upgrade or alternative extractor — track them as backlog. |

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