MultiPhysicsVault/skills/wiki-ingest/SKILL.md

name, description

name	description
wiki-ingest	Ingest sources into the Obsidian wiki vault. Reads a source, extracts entities and concepts, creates or updates wiki pages, cross-references, and logs the operation. Supports files, URLs, and batch mode. Triggers on: ingest, process this source, add this to the wiki, read and file this, batch ingest, ingest all of these, ingest this url.

wiki-ingest: Source Ingestion

Read the source. Write the wiki. Cross-reference everything. A single source typically touches 8-15 wiki pages.

Syntax standard: Write all Obsidian Markdown using proper Obsidian Flavored Markdown. Wikilinks as [[Note Name]], callouts as > [!type] Title, embeds as ![[file]], properties as YAML frontmatter. If the kepano/obsidian-skills plugin is installed, prefer its canonical obsidian-markdown skill for Obsidian syntax reference. Otherwise, follow the guidance in this skill.

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Transport (v1.7+)

Before mutating any vault file, consult .vault-meta/transport.json (auto-created by bash scripts/detect-transport.sh). Use the preferred transport per the fallback chain:

• cli — obsidian-cli write "$VAULT" "$NOTE" < content.md (or append, property:set); see skills/wiki-cli/SKILL.md
• mcp-obsidian / mcpvault — mcp__obsidian-vault__write_note and friends; see skills/wiki/references/mcp-setup.md
• filesystem — Claude's Write/Edit tools with absolute vault-rooted paths (final floor; always works)

Full decision tree: wiki/references/transport-fallback.md.

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Mode awareness (v1.8+)

Before creating any new wiki page, consult the vault's methodology mode via python3 scripts/wiki-mode.py route <type> "<name>". The router returns the vault-relative path where the page should be filed.

SRC_PATH=$(python3 scripts/wiki-mode.py route source "Karpathy 2025 LLM Wiki essay")
# generic:      wiki/sources/Karpathy-2025-LLM-Wiki-essay.md
# lyt:          wiki/notes/Karpathy-2025-LLM-Wiki-essay.md  (also update relevant MOC)
# para:         wiki/resources/incoming/Karpathy-2025-LLM-Wiki-essay.md
# zettelkasten: wiki/20260517123456-Karpathy-2025-LLM-Wiki-essay.md

ENT_PATH=$(python3 scripts/wiki-mode.py route entity "Andrej Karpathy")
CON_PATH=$(python3 scripts/wiki-mode.py route concept "Compounding Vault Pattern")

If .vault-meta/mode.json is absent, the router returns mode=generic paths (identical to v1.7 behavior). No special-casing needed in this skill.

Mode-specific follow-up:

• LYT: after filing the atomic note, update the relevant MOC (wiki/mocs/<topic>-moc.md) to link the new note. If no MOC exists for the topic, create one using skills/wiki-mode/templates/lyt/moc-template.md.
• Zettelkasten: filename already includes the timestamp ID. Populate the id: frontmatter field to match.
• PARA: new ingests land in wiki/resources/incoming/ by default. Do NOT auto-guess the topic; leave in incoming/ for user review.

Concurrency (v1.7+)

Multi-writer is safe in v1.7. The latent corruption bug from v1.6 — where two parallel sub-agents writing to the same page could silently trample each other — is closed by per-file advisory locking. Every wiki page write MUST be preceded by wiki-lock acquire <path>.

# Acquire — blocks (returns 75 EX_TEMPFAIL) if another writer holds the lock
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: another writer is in flight. Retry once after 2s; if still held,
  # log to wiki/log.md and skip this page rather than overwrite.
  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); logged to wiki/log.md"
fi

Properties:

• Per-file granularity. Locks key on sha1(<vault-relative-path>); concurrent writes to DIFFERENT pages run in parallel.
• Age-based staleness. Default STALE_AFTER_SEC=60. A crashed holder unblocks in ≤60 seconds without manual intervention. See scripts/wiki-lock.sh header for the full semantics.
• Cross-process release. Release is rm -f (no PID match required). Skill authors are trusted to release locks they acquire; cross-skill release is allowed by design (a janitor running wiki-lock clear-stale --max-age 0 is the canonical recovery path).
• The PostToolUse hook now defers git add if any locks are currently held, so the auto-commit doesn't fire mid-ingest and produce torn commits. See hooks/hooks.json.

wiki-lock is unconditional in v1.7+ — there is no feature gate, no fallback. Skills that don't acquire locks are racing against any other writer. The script is in core, not opt-in.

Sub-agent rule from v1.6 — "Sub-agents MUST NOT call scripts/allocate-address.sh" — is preserved (orchestrator still backfills addresses to keep the counter monotonic). The NEW rule is: sub-agents MAY now write pages, but MUST acquire locks first. See agents/wiki-ingest.md.

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Delta Tracking

Before ingesting any file, check .raw/.manifest.json to avoid re-processing unchanged sources.

# Check if manifest exists
[ -f .raw/.manifest.json ] && echo "exists" || echo "no manifest yet"

Manifest format (create if missing):

{
  "sources": {
    ".raw/articles/article-slug-2026-04-08.md": {
      "hash": "abc123",
      "ingested_at": "2026-04-08",
      "pages_created": ["wiki/sources/article-slug.md", "wiki/entities/Person.md"],
      "pages_updated": ["wiki/index.md"]
    }
  }
}

Before ingesting a file:

1. Compute a hash: md5sum [file] | cut -d' ' -f1 (or sha256sum on Linux).
2. Check if the path exists in .manifest.json with the same hash.
3. If hash matches, skip. Report: "Already ingested (unchanged). Use force to re-ingest."
4. If missing or hash differs, proceed with ingest.

After ingesting a file:

1. Record {hash, ingested_at, pages_created, pages_updated} in .manifest.json.
2. Write the updated manifest back.

Skip delta checking if the user says "force ingest" or "re-ingest".

---

URL Ingestion

Trigger: user passes a URL starting with https://.

Steps:

1. Fetch the page using WebFetch.
2. Clean (optional): if defuddle is available (which defuddle 2>/dev/null), run defuddle [url] to strip ads, nav, and clutter. Typically saves 40-60% tokens. Fall back to raw WebFetch output if not installed.
3. Derive slug from the URL path (last segment, lowercased, spaces→hyphens, strip query strings).
4. Save to .raw/articles/[slug]-[YYYY-MM-DD].md with a frontmatter header:

   ---
   source_url: [url]
   fetched: [YYYY-MM-DD]
   ---
   

5. Proceed with Single Source Ingest starting at step 2 (file is now in .raw/).

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Image / Vision Ingestion

Trigger: user passes an image file path (.png, .jpg, .jpeg, .gif, .webp, .svg, .avif).

Steps:

1. Read the image file using the Read tool. Claude can process images natively.
2. Describe the image contents: extract all text (OCR), identify key concepts, entities, diagrams, and data visible in the image.
3. Save the description to .raw/images/[slug]-[YYYY-MM-DD].md:

   ---
   source_type: image
   original_file: [original path]
   fetched: YYYY-MM-DD
   ---
   # Image: [slug]
   
   [Full description of image contents, transcribed text, entities visible, etc.]
   

4. Copy the image to _attachments/images/[slug].[ext] if it's not already in the vault.
5. Proceed with Single Source Ingest on the saved description file.

Use cases: whiteboard photos, screenshots, diagrams, infographics, document scans.

---

Single Source Ingest

Trigger: user drops a file into .raw/ or pastes content.

Steps:

1. Read the source completely. Do not skim.
2. Discuss key takeaways with the user. Ask: "What should I emphasize? How granular?" Skip this if the user says "just ingest it."
3. Create source summary in wiki/sources/. Use the source frontmatter schema from references/frontmatter.md. Assign an address per the Address Assignment section below.
4. Create or update entity pages for every person, org, product, and repo mentioned. One page per entity. Assign addresses to new entity pages.
5. Create or update concept pages for significant ideas and frameworks. Assign addresses to new concept pages.
6. Update relevant domain page(s) and their _index.md sub-indexes.
7. Update wiki/overview.md if the big picture changed.
8. Update wiki/index.md. Add entries for all new pages.
9. Update wiki/hot.md with this ingest's context.
10. Append to wiki/log.md (new entries at the TOP):

    ## [YYYY-MM-DD] ingest | Source Title
    - Source: `.raw/articles/filename.md`
    - Summary: [[Source Title]]
    - Pages created: [[Page 1]], [[Page 2]]
    - Pages updated: [[Page 3]], [[Page 4]]
    - Key insight: One sentence on what is new.
    

11. Check for contradictions. If new info conflicts with existing pages, add > [!contradiction] callouts on both pages.

---

Batch Ingest

Trigger: user drops multiple files or says "ingest all of these."

Steps:

1. List all files to process. Confirm with user before starting.
2. Process each source following the single ingest flow. Defer cross-referencing between sources until step 3.
3. After all sources: do a cross-reference pass. Look for connections between the newly ingested sources.
4. Update index, hot cache, and log once at the end (not per-source).
5. Report: "Processed N sources. Created X pages, updated Y pages. Here are the key connections I found."

Batch ingest is less interactive. For 30+ sources, expect significant processing time. Check in with the user after every 10 sources.

---

Context Window Discipline

Token budget matters. Follow these rules during ingest:

• Read wiki/hot.md first. If it contains the relevant context, don't re-read full pages.
• Read wiki/index.md to find existing pages before creating new ones.
• Read only 3-5 existing pages per ingest. If you need 10+, you are reading too broadly.
• Use PATCH for surgical edits. Never re-read an entire file just to update one field.
• Keep wiki pages short. 100-300 lines max. If a page grows beyond 300 lines, split it.
• Use search (/search/simple/) to find specific content without reading full pages.

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Contradictions

[!note] Custom callout dependency The [!contradiction] callout type used below is a custom callout defined in .obsidian/snippets/vault-colors.css (auto-installed by /wiki scaffold). It renders with reddish-brown styling and an alert-triangle icon when the snippet is enabled. If the snippet is missing, Obsidian falls back to default callout styling, so the page still works without the visual flourish. See skills/wiki/references/css-snippets.md for the four custom callouts (contradiction, gap, key-insight, stale).

When new info contradicts an existing wiki page:

On the existing page, add:

> [!contradiction] Conflict with [[New Source]]
> [[Existing Page]] claims X. [[New Source]] says Y.
> Needs resolution. Check dates, context, and primary sources.

On the new source summary, reference it:

> [!contradiction] Contradicts [[Existing Page]]
> This source says Y, but existing wiki says X. See [[Existing Page]] for details.

Do not silently overwrite old claims. Flag and let the user decide.

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What Not to Do

• Source files under .raw/ are immutable. Do not modify the files that users drop there (articles, transcripts, images). The .raw/.manifest.json delta tracker and its address_map (DragonScale Mechanism 2) are the only files under .raw/ that wiki-ingest itself maintains. Treat every other file under .raw/ as read-only source content.
• Do not create duplicate pages. Always check the index and search before creating.
• Do not skip the log entry. Every ingest must be recorded.
• Do not skip the hot cache update. It is what keeps future sessions fast.

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Address Assignment (DragonScale Mechanism 2 MVP)

Opt-in feature. DragonScale address assignment runs only if scripts/allocate-address.sh is present AND .vault-meta/ exists. Otherwise, skip this entire section and proceed with ingest normally.

Feature detection (run at start of every ingest):

if [ -x ./scripts/allocate-address.sh ] && [ -d ./.vault-meta ]; then
  DRAGONSCALE_ADDRESSES=1
else
  DRAGONSCALE_ADDRESSES=0
fi

When DRAGONSCALE_ADDRESSES=0, pages are created without an address: frontmatter field, and wiki-lint's Address Validation section is skipped entirely (missing addresses are not flagged in any severity). This preserves default plugin behavior for vaults that have not adopted DragonScale.

When DRAGONSCALE_ADDRESSES=1, proceed with the rest of this section.

---

Every newly created non-meta wiki page gets a stable address in its frontmatter:

address: c-000042

Format: c-<6-digit-counter>. The c- prefix stands for "creation-order counter." Zero-padded.

Rollout baseline: 2026-04-23 (Phase 2 ship date). Pages with created: >= this date are post-rollout and MUST have an address (unless excluded below). Pages with created: earlier are legacy-exempt until a deliberate backfill pass assigns l-NNNNNN addresses.

Required tool: scripts/allocate-address.sh

Address allocation is delegated to an atomic Bash helper. The helper uses flock on .vault-meta/.address.lock to prevent read-use-increment races and recovers the counter by scanning existing frontmatter if the counter file is missing.

ADDR=$(./scripts/allocate-address.sh)
# ADDR is now e.g. "c-000042"; counter is already incremented

CRITICAL: never use the Write or Edit tool on .vault-meta/address-counter.txt. That would fire the PostToolUse hook, which runs git add wiki/ .raw/ and can accidentally commit unrelated pending wiki changes under a generic message. Counter mutation is only permitted through the helper script (Bash tool).

Helper modes

• ./scripts/allocate-address.sh — atomically reserves and returns the next address.
• ./scripts/allocate-address.sh --peek — prints the next value without reserving (safe, read-only).
• ./scripts/allocate-address.sh --rebuild — recomputes the counter from the highest observed c-NNNNNN in existing frontmatter. Never resets to 1 silently if pages already have addresses. Run this if the counter file is suspected corrupt.

Assignment procedure (per new page)

1. Before writing a new non-meta page, call ./scripts/allocate-address.sh and capture the output.
2. Include address: c-XXXXXX in the page's frontmatter.
3. Record the path-to-address mapping in .raw/.manifest.json under a new top-level key address_map (see schema below).

address_map in .raw/.manifest.json

{
  "sources": { ... },
  "address_map": {
    "wiki/concepts/Example.md": "c-000042",
    "wiki/entities/Another.md": "c-000043"
  }
}

On re-ingest of the same source (whether by --force or a changed hash), always consult address_map first. If the target page path has a prior address, REUSE it. Do not allocate a new one.

On a page rename, the skill must update the address_map key (old path -> new path) while preserving the address value.

Exclusions (do NOT assign an address to)

• Meta files: _index.md, index.md, log.md, hot.md, overview.md, dashboard.md, dashboard.base, Wiki Map.md, getting-started.md.
• Fold pages under wiki/folds/ (they use their own deterministic fold_id).
• Pre-rollout legacy pages (created: < 2026-04-23). Legacy pages get l-NNNNNN addresses only via a deliberate backfill operation.

Idempotency rules

• If a page being (re)written already has an address: field in its current content, REUSE it. Do not allocate a new one.
• If a source is re-ingested and address_map has a mapping for the target path, reuse that mapping.
• If the source has been ingested before AND the target page has no address AND the page created: date is post-rollout, allocate an address and record it. This covers the case where an older ingest produced a page before Phase 2 rollout; the rollout cutoff still applies (pages dated pre-2026-04-23 stay legacy).

Concurrency policy

• Single-writer only in Phase 2. Do not run parallel ingests from multiple Claude sessions or sub-agents that assign addresses. The flock in the helper prevents counter corruption but does not serialize page writes themselves.
• Sub-agents (codex, general-purpose) that are dispatched for research or review MUST NOT call the allocator. They are read-only in this respect.
• Multi-writer support is a deferred feature.

Batch ingest

Assign addresses sequentially during single-source-ingest for each source. Do not pre-reserve a block of counter values. The helper is cheap (one lock, one integer read/write).

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How to think (10-principle mapping)

When working on this skill, apply the 10-principle loop. See skills/think/SKILL.md for the canonical framework.

#	Principle	Application here
1	OBSERVE (ext)	Read the source file completely before extracting anything. No shortcuts on long sources.
2	OBSERVE (int)	Am I biased toward the source's framing? Where do my disagreements live? Note them as contradiction callouts.
3	LISTEN	The user's source-selection intent — what made THIS source worth ingesting, and what is the user hoping to extract?
4	THINK	Which entities deserve pages? Which concepts? What cross-references? What contradictions with existing pages?
5	CONNECT (lat)	This source's claims vs other sources already in the wiki. Contradictions are the highest-signal finding.
6	CONNECT (sys)	wiki-mode.py route for paths + wiki-lock.sh for safety + index/log/hot for consumer visibility.
7	FEEL	A page that compounds — useful in 6 months, not just today. Skip filler; favor synthesis over transcription.
8	ACCEPT	Not every claim is wiki-worthy. Editorial judgment is part of ingest, not a bug to remove.
9	CREATE	Source + entity + concept pages with full frontmatter; cross-references; contradiction callouts where needed.
10	GROW	Contradictions found mid-ingest are the most valuable wiki signal. File them as questions for follow-up, not silently.