FESADev/PROGRESS.md

# PROGRESS

## Purpose
`PROGRESS.md` is the shared chronological status log for FESA agents.

Every new agent session must read this file together with `PLAN.md` before planning or editing. Keep this file factual: what changed, what was verified, what is blocked, and what remains risky.

## How To Use
- Add a new entry whenever a meaningful planning, documentation, implementation, verification, or review task is completed.
- Include date, agent or author when known, changed files, verification performed, and follow-up items.
- Record blockers explicitly.
- Do not use this file as a future task list. Put future tasks in `PLAN.md`.
- Do not remove history unless the user explicitly asks for archival cleanup.

## Current Status
Phase 1 has a new rebaseline phase definition in `phases/1-linear-static-mitc4-rebaseline`. Step 0 is complete and captured in `phases/1-linear-static-mitc4-rebaseline/step0-audit.md`. The old `phases/1-linear-static-mitc4` path is historical and superseded after the MITC4 formulation reset. P1-01 through P1-14 have an initial C++17 implementation, but it is no longer authoritative until each layer is revalidated against the revised paper-based `docs/MITC4_FORMULATION.md`. `quad_02` is now the stored S4 reference pair, but its `Part/Assembly/Instance` and `*Density` features remain a compatibility decision for rebaseline step 1.

## Completed Work

### 2026-05-04 - P1R-00 rebaseline audit completed
Author: Codex

Changed files:
- `phases/1-linear-static-mitc4-rebaseline/step0-audit.md`
- `phases/1-linear-static-mitc4-rebaseline/index.json`
- `PLAN.md`
- `PROGRESS.md`

Summary:
- Audited the existing C++ Phase 1 implementation against the revised paper-based `docs/MITC4_FORMULATION.md` without changing production solver behavior.
- Classified reusable scaffolding for revalidation: CMake/CTest validation, core aliases, DOF mapping, diagnostics, parser/domain skeleton, in-memory `U`/`RF` results, displacement CSV comparator, full-vector reaction recovery, and the linear static workflow.
- Identified MITC4 conflicts requiring rebuild: averaged-edge local basis, 2D projected Jacobian, direct Cartesian-like shear row construction, membrane/bending/shear pre-integration, midsurface-only `2 x 2` integration, and old `1.0e-6` drilling stabilization.
- Preserved the compatibility decision that `quad_02.inp` is an S4 reference artifact but still contains `Part/Assembly/Instance` and `*Density`, so Step 1 must choose a normalized-input or explicit parser-compatibility path.

Verification:
- Inspected `include/fesa/fesa.hpp`, `tests/test_main.cpp`, current reference files, and active rebaseline phase contracts.
- `python scripts/validate_workspace.py` configured CMake, built `fesa_core` and `fesa_tests`, and ran CTest successfully.

Follow-up:
- Continue with P1R-01 reference onboarding.
- Revalidate retained scaffolding in its assigned steps before treating it as Phase 1 evidence.

### 2026-05-04 - Phase 1 rebaseline steps redefined
Author: Codex

Changed files:
- `phases/index.json`
- `phases/1-linear-static-mitc4-rebaseline/index.json`
- `phases/1-linear-static-mitc4-rebaseline/step0.md`
- `phases/1-linear-static-mitc4-rebaseline/step1.md`
- `phases/1-linear-static-mitc4-rebaseline/step2.md`
- `phases/1-linear-static-mitc4-rebaseline/step3.md`
- `phases/1-linear-static-mitc4-rebaseline/step4.md`
- `phases/1-linear-static-mitc4-rebaseline/step5.md`
- `phases/1-linear-static-mitc4-rebaseline/step6.md`
- `phases/1-linear-static-mitc4-rebaseline/step7.md`
- `phases/1-linear-static-mitc4-rebaseline/step8.md`
- `phases/1-linear-static-mitc4-rebaseline/step9.md`
- `phases/1-linear-static-mitc4-rebaseline/step10.md`
- `phases/1-linear-static-mitc4-rebaseline/step11.md`
- `phases/1-linear-static-mitc4-rebaseline/step12.md`
- `phases/1-linear-static-mitc4-rebaseline/step13.md`
- `phases/1-linear-static-mitc4-rebaseline/step14.md`
- `phases/1-linear-static-mitc4-rebaseline/step15.md`
- `PLAN.md`
- `PROGRESS.md`

Summary:
- Added a new 16-step Phase 1 rebaseline phase that supersedes the old Phase 1 execution path while preserving the old phase as historical record.
- Split the redo into audit, reference onboarding, core guardrails, parser/domain, validation diagnostics, DOF/reaction foundation, results/comparator, MITC4 geometry, MITC4 covariant strain tying, material/integration, stiffness/drilling, patch benchmarks, assembly, linear static workflow, stored-reference regression, and evaluator closeout.
- Updated `PLAN.md` so new agents execute `phases/1-linear-static-mitc4-rebaseline` and treat the old `1-linear-static-mitc4` phase as blocked/superseded.
- Kept unresolved decisions visible: `quad_02` normalization versus explicit parser compatibility sprint, RF CSV availability, and the PRD target of three stored Phase 1 reference cases.

Verification:
- Parsed `phases/index.json` and `phases/1-linear-static-mitc4-rebaseline/index.json` with PowerShell `ConvertFrom-Json`.
- Verified all 16 rebaseline step files contain the required sprint contract sections from `docs/HARNESS_ENGINEERING.md`.
- `python scripts/validate_workspace.py` configured CMake, built `fesa_core` and `fesa_tests`, and ran CTest successfully.
- CTest result: 1 test executable passed.

Follow-up:
- Start with `python scripts/execute.py 1-linear-static-mitc4-rebaseline` when ready.
- Step 1 must resolve how to use `quad_02` without silently expanding parser support.

### 2026-05-04 - MITC4 formulation reset from local papers
Author: Codex

Changed files:
- `docs/Paper/`
- `docs/MITC4_FORMULATION.md`
- `docs/ADR.md`
- `docs/NUMERICAL_CONVENTIONS.md`
- `docs/README.md`
- `docs/ABAQUS_INPUT_SUBSET.md`
- `docs/VERIFICATION_PLAN.md`
- `references/quad_02.inp`
- `references/quad_02_displacements.csv`
- `PLAN.md`
- `PROGRESS.md`

Summary:
- Read the local MITC4 paper set under `docs/Paper/` and rewrote `docs/MITC4_FORMULATION.md` as the new Phase 1 formulation contract.
- Replaced the earlier simplified baseline with degenerated-continuum geometry, convected covariant strain components, FESA/Abaqus S4 tying-point convention, MITC transverse shear interpolation, local/global six-DOF rotation transformation, `2 x 2 x 2` Gauss integration, and thesis-backed drilling stabilization using `drilling_stiffness_scale = 1.0e-3`.
- Updated ADR-018, numerical conventions, and documentation readiness notes so the old `1.0e-6` averaged-edge baseline is no longer the active rule.
- Recorded `quad_02` as the new stored S4 reference pair while keeping its `Part/Assembly/Instance` and `*Density` features outside automatic Phase 1 parser acceptance.
- Updated `PLAN.md` so the next work is a Phase 1 redo/rebaseline, not continuation of the old P1-15/P1-16 path.

Verification:
- `python scripts/validate_workspace.py` configured CMake, built `fesa_core` and `fesa_tests`, and ran CTest successfully.
- CTest result: 1 test executable passed.

Follow-up:
- Draft new Phase 1 redo sprint contracts against the revised MITC4 formulation before modifying solver code.
- Decide whether `quad_02.inp` should be normalized into the current parser subset or used to justify a dedicated Abaqus/CAE `Part/Assembly/Instance` parser sprint.
- Decide whether Phase 1 `RF` gets Abaqus `*_reactions.csv` artifacts or remains verified by full-vector equilibrium tests.

### 2026-05-01 - P1-01 through P1-14 implementation pass
Author: Codex

Changed files:
- `CMakeLists.txt`
- `include/fesa/fesa.hpp`
- `src/fesa.cpp`
- `tests/test_main.cpp`
- `scripts/validate_workspace.py`
- `README.md`
- `docs/ADR.md`
- `docs/MITC4_FORMULATION.md`
- `PLAN.md`
- `PROGRESS.md`
- `phases/index.json`
- `phases/1-linear-static-mitc4/index.json`

Summary:
- Added a CMake/CTest C++17 build and test harness, and updated `scripts/validate_workspace.py` to run CMake configure, build, and CTest directly.
- Added core numeric aliases, DOF mapping, diagnostics, Domain entities, Abaqus Phase 1 parser, Domain validation, DofManager, dense test matrix, deterministic Gaussian solver, in-memory result model, displacement CSV loader/comparator, MITC4 baseline stiffness kernel, full-system assembly, and `LinearStaticAnalysis`.
- Closed the Phase 1 MITC4 baseline decisions in `docs/MITC4_FORMULATION.md`: midside shear tying interpolation, averaged-edge local basis, 2x2 integration, `drilling_stiffness_scale = 1.0e-6`, and mandatory `U`/`RF` output scope.
- Added ADR-017 for the CMake/CTest build harness and ADR-018 for the Phase 1 MITC4 baseline closure.
- Added tests for parser acceptance/rejection, `quad_01` unsupported provenance, validation diagnostics, DOF reconstruction, singular solve diagnostics, result fields, CSV loading/comparison, MITC4 shape/stiffness behavior, and end-to-end linear static RF recovery.
- Marked phase steps P1-01 through P1-14 completed in `phases/1-linear-static-mitc4/index.json`.
- Marked P1-15 blocked because no Phase 1-compatible Abaqus S4 reference case exists yet; P1-16 remains pending behind that blocker.

Verification:
- `python scripts/validate_workspace.py` configured CMake, built `fesa_core` and `fesa_tests`, and ran CTest successfully.
- CTest result: 1 test executable passed, covering 12 named in-repo test cases.

Follow-up:
- Add at least one Phase 1-compatible Abaqus `TYPE=S4` linear static input and matching `*_displacements.csv`.
- Add or explicitly defer `*_reactions.csv`; current RF validation is by internal full-vector equilibrium/reaction tests.
- After reference artifacts are added, unblock P1-15 and run stored-reference regression, then complete P1-16 evaluator closeout.

### 2026-05-01 - P1-00 Phase 1 sprint contracts generated
Author: Codex

Changed files:
- `phases/index.json`
- `phases/1-linear-static-mitc4/index.json`
- `phases/1-linear-static-mitc4/step0.md`
- `phases/1-linear-static-mitc4/step1.md`
- `phases/1-linear-static-mitc4/step2.md`
- `phases/1-linear-static-mitc4/step3.md`
- `phases/1-linear-static-mitc4/step4.md`
- `phases/1-linear-static-mitc4/step5.md`
- `phases/1-linear-static-mitc4/step6.md`
- `phases/1-linear-static-mitc4/step7.md`
- `phases/1-linear-static-mitc4/step8.md`
- `phases/1-linear-static-mitc4/step9.md`
- `phases/1-linear-static-mitc4/step10.md`
- `phases/1-linear-static-mitc4/step11.md`
- `phases/1-linear-static-mitc4/step12.md`
- `phases/1-linear-static-mitc4/step13.md`
- `phases/1-linear-static-mitc4/step14.md`
- `phases/1-linear-static-mitc4/step15.md`
- `PLAN.md`
- `PROGRESS.md`

Summary:
- Converted Phase 1 milestones P1-01 through P1-16 into executable Harness step files under `phases/1-linear-static-mitc4`.
- Added top-level and phase-level JSON indices using the zero-based `scripts/execute.py` convention.
- Embedded sprint contracts in every step with objective, required reading, scope, allowed files, explicit non-goals, tests to write first, reference-artifact policy, acceptance command, evaluator checklist, and handoff requirements.
- Kept readiness blockers visible, especially MITC4 formulation decisions, build-system selection, reference comparator tolerance, missing reaction CSV, and the need for Phase 1-compatible `TYPE=S4` references.
- Updated `PLAN.md` so new agents can find and execute the active phase files.

Verification:
- Parsed `phases/index.json` and `phases/1-linear-static-mitc4/index.json` with PowerShell `ConvertFrom-Json`.
- Verified the phase registry points to `1-linear-static-mitc4`, all 16 steps are `pending`, step names are kebab-case, and every `stepN.md` file exists.
- Verified every step file includes the required sprint contract sections from `docs/HARNESS_ENGINEERING.md`.
- `python scripts/validate_workspace.py` exited successfully, but still reported no configured validation commands.

Follow-up:
- Begin Phase 1 execution with `python scripts/execute.py 1-linear-static-mitc4` after confirming readiness blockers are accepted, resolved, or intentionally deferred.

### 2026-05-01 - Phase 1 implementation master plan added
Author: Codex

Changed files:
- `PLAN.md`
- `PROGRESS.md`

Summary:
- Expanded `PLAN.md` from a short implementation sequence into a Phase 1 master implementation plan.
- Added Phase 1 Definition of Done, execution gates, milestone backlog P1-00 through P1-16, sprint contract rules, verification strategy, reference plan, and risk controls.
- Kept implementation blocked behind readiness decisions for MITC4 formulation, build system, reference comparator, reaction verification, and Phase 1-compatible reference input.
- Aligned the plan with the Planner -> Generator -> Evaluator harness in `docs/HARNESS_ENGINEERING.md`.

Verification:
- Reviewed the plan against `docs/PRD.md`, `docs/ARCHITECTURE.md`, `docs/HARNESS_ENGINEERING.md`, `docs/NUMERICAL_CONVENTIONS.md`, `docs/ABAQUS_INPUT_SUBSET.md`, `docs/VERIFICATION_PLAN.md`, `docs/RESULTS_SCHEMA.md`, and `docs/MITC4_FORMULATION.md`.
- `python scripts/validate_workspace.py` ran, but reported no configured validation commands.

Follow-up:
- Convert P1 milestones into `phases/` step files with sprint contract sections when the user asks for executable phase planning.

### 2026-05-01 - Planner/Generator/Evaluator harness structure added
Author: Codex

Changed files:
- `AGENTS.md`
- `PLAN.md`
- `PROGRESS.md`
- `README.md`
- `docs/README.md`
- `docs/HARNESS_ENGINEERING.md`
- `docs/MULTI_AGENT_RESEARCH_PLAN.md`
- `.codex/agents/harness-sprint-planner.toml`
- `.codex/agents/implementation-generator.toml`
- `.codex/agents/harness-sprint-evaluator.toml`
- `.codex/agents/phase-planner.toml`
- `.codex/agents/harness-reviewer.toml`
- `.codex/agents/test-strategy-reviewer.toml`
- `.codex/skills/fesa-phase-planning/SKILL.md`
- `.codex/skills/fesa-review/SKILL.md`
- `.codex/skills/fesa-cpp-tdd/SKILL.md`
- `plugins/fesa-commands/commands/phase-draft.md`

Summary:
- Added `docs/HARNESS_ENGINEERING.md` as the durable Planner -> Generator -> Evaluator contract for long-running FESA work.
- Updated `AGENTS.md` so nontrivial solver, parser, result schema, reference comparator, MITC4, and phase execution work requires a sprint contract before implementation.
- Added custom agents for sprint contract planning, contract-bound implementation, and independent sprint evaluation.
- Updated existing planner/reviewer/test strategy guidance to enforce contract compliance, evaluator pass/fail review, TDD, and PLAN/PROGRESS handoff.

Verification:
- `.codex/agents/*.toml` parsed successfully with Python `tomllib`.
- Codex skill and plugin command frontmatter checks passed.
- `python scripts/validate_workspace.py` ran, but reported no configured validation commands.

Follow-up:
- When implementation planning begins, generate phase steps with sprint contract sections before assigning Generator work.

### 2026-05-01 - Abaqus reference CSV contract adopted
Author: Codex

Changed files:
- `AGENTS.md`
- `README.md`
- `PLAN.md`
- `PROGRESS.md`
- `docs/README.md`
- `docs/PRD.md`
- `docs/ARCHITECTURE.md`
- `docs/ADR.md`
- `docs/NUMERICAL_CONVENTIONS.md`
- `docs/ABAQUS_INPUT_SUBSET.md`
- `docs/VERIFICATION_PLAN.md`
- `docs/RESULTS_SCHEMA.md`
- `docs/MITC4_FORMULATION.md`
- `docs/MULTI_AGENT_RESEARCH_PLAN.md`
- `references/README.md`
- `.codex/agents/*.toml`
- `.codex/skills/*.md`
- `plugins/fesa-commands/commands/*.md`

Summary:
- Accepted `references/` as the project reference artifact root.
- Documented the initial artifact pair `references/quad_01.inp` and `references/quad_01_displacements.csv`.
- Adopted Abaqus-exported `*_displacements.csv` as the first automated displacement comparison format.
- Mapped CSV columns `Node Label`, `U-U1`, `U-U2`, `U-U3`, `UR-UR1`, `UR-UR2`, `UR-UR3` to FESA `U` components `UX`, `UY`, `UZ`, `RX`, `RY`, `RZ`.
- Documented that `quad_01.inp` includes `S4R`, `Part/Assembly/Instance`, `*Density`, and `NLGEOM=YES`; it is stored reference provenance and a future compatibility target, not a Phase 1 parser acceptance expansion.

Verification:
- Inspected `quad_01_displacements.csv`: 121 data rows and the required Abaqus displacement/rotation columns.
- Parsed documentation and Codex extension metadata checks.
- `python scripts/validate_workspace.py` ran, but reported no configured validation commands.

Follow-up:
- Add or define reaction-force reference artifacts, preferably `*_reactions.csv`, or verify `RF` by equilibrium tests until Abaqus RF CSV is available.
- Add at least one Phase 1-compatible `TYPE=S4` reference input for the first MITC4 linear static implementation path.

### 2026-05-01 - FESA commands converted to repo plugin
Author: Codex

Changed files:
- `plugins/fesa-commands/.codex-plugin/plugin.json`
- `plugins/fesa-commands/commands/*.md`
- `.agents/plugins/marketplace.json`
- `.codex/commands/*.md`
- `.codex/hooks/pre_edit_policy.py`
- `.codex/hooks/post_tool_use_policy.py`
- `PLAN.md`
- `PROGRESS.md`

Summary:
- Created the repo-local `fesa-commands` plugin and registered it in `.agents/plugins/marketplace.json`.
- Moved the FESA command prompts from `.codex/commands/` into `plugins/fesa-commands/commands/`.
- Removed the old `.codex/commands/*.md` files so plugin commands are the single maintained location.
- Updated hook policy scripts to watch plugin manifests, plugin commands, and marketplace registration files.
- Resolved the prior `.codex/commands` discovery concern by converting the commands to plugin form.

Verification:
- Parsed plugin manifests and `.agents/plugins/marketplace.json` with Python `json`.
- Checked plugin command Markdown frontmatter.
- Parsed `.codex/config.toml` and `.codex/agents/*.toml` with Python `tomllib`.
- Parsed `.codex/hooks.json` with Python `json`.
- `python scripts/validate_workspace.py` ran, but reported no configured validation commands.

Follow-up:
- Confirm that the `fesa-commands` plugin appears in the active Codex plugin/command surface.

### 2026-05-01 - Project-local Codex extension pack added
Author: Codex

Changed files:
- `.codex/config.toml`
- `.codex/hooks.json`
- `.codex/agents/*.toml`
- `.codex/commands/*.md`
- `.codex/skills/*/SKILL.md`
- `.codex/hooks/*.py`
- `PLAN.md`
- `PROGRESS.md`

Summary:
- Added focused project agents for reference artifact curation, numerical convention review, solver architecture, sparse solver design, HDF5 results schema, DOF/boundary conditions, C++ build planning, MITC4 implementation review, test strategy, and PLAN/PROGRESS auditing.
- Added project command prompts for status, readiness, plan sync, reference checks, documentation guards, phase drafting, ADR work, benchmark onboarding, extension verification, and handoff.
- Added project-local FESA skills and registered them through `.codex/config.toml`.
- Added hooks for session startup context, pre-edit coordination reminders, post-edit validation reminders, and expanded destructive shell command blocking.

Verification:
- Parsed `.codex/config.toml` and `.codex/agents/*.toml` with Python `tomllib`.
- Parsed `.codex/hooks.json` with Python `json`.
- Checked `.codex/skills/*/SKILL.md` and `.codex/commands/*.md` frontmatter.
- Smoke-tested the new hook scripts with representative JSON payloads.
- `python scripts/validate_workspace.py` ran, but reported no configured validation commands.

Follow-up:
- Resolved later by converting `.codex/commands/*.md` into the `fesa-commands` repo plugin.
- Confirm hook behavior in the actual Codex runtime on native Windows.

### 2026-05-01 - PLAN/PROGRESS coordination files added
Author: Codex

Changed files:
- `PLAN.md`
- `PROGRESS.md`
- `AGENTS.md`
- `docs/README.md`
- `docs/MULTI_AGENT_RESEARCH_PLAN.md`
- `.codex/agents/phase-planner.toml`
- `.codex/agents/harness-reviewer.toml`

Summary:
- Added `PLAN.md` as the shared forward-looking work plan for multi-agent coordination.
- Added `PROGRESS.md` as the shared chronological progress, verification, blocker, and risk log.
- Updated `AGENTS.md` so every new work session must read `PROGRESS.md` and `PLAN.md` before planning or editing.
- Updated documentation index and Codex agent instructions so planning/review agents enforce PLAN/PROGRESS usage.

Verification:
- `.codex/agents/*.toml` parsed successfully with Python `tomllib`.
- `python scripts/validate_workspace.py` ran, but reported no configured validation commands.

### 2026-05-01 - Documentation coordination and multi-agent planning state
Author: Codex

Changed files:
- `AGENTS.md`
- `README.md`
- `docs/README.md`
- `docs/PRD.md`
- `docs/ARCHITECTURE.md`
- `docs/ADR.md`
- `docs/NUMERICAL_CONVENTIONS.md`
- `docs/ABAQUS_INPUT_SUBSET.md`
- `docs/VERIFICATION_PLAN.md`
- `docs/RESULTS_SCHEMA.md`
- `docs/MITC4_FORMULATION.md`
- `docs/MULTI_AGENT_RESEARCH_PLAN.md`
- `.codex/agents/*.toml`

Summary:
- Added `docs/README.md` as documentation index and implementation readiness gate.
- Reinforced Phase 1 invariants across project docs.
- Added readiness gates for numerical conventions, parser acceptance, reference onboarding, mandatory result outputs, and MITC4 pre-implementation decisions.
- Updated Codex agent definitions so delegated agents read the current documentation set.
- Root `README.md` now points to the FESA documentation entry point.

Verification:
- `.codex/agents/*.toml` parsed successfully with Python `tomllib`.
- `python scripts/validate_workspace.py` ran, but reported no configured validation commands.

Follow-up:
- Keep `PLAN.md` and `PROGRESS.md` current for multi-agent coordination.

### 2026-04-22 - Technical dossier documents added
Author: Codex

Changed files:
- `docs/NUMERICAL_CONVENTIONS.md`
- `docs/ABAQUS_INPUT_SUBSET.md`
- `docs/VERIFICATION_PLAN.md`
- `docs/RESULTS_SCHEMA.md`
- `docs/MITC4_FORMULATION.md`
- `AGENTS.md`
- `docs/PRD.md`
- `docs/ARCHITECTURE.md`
- `docs/ADR.md`
- `docs/MULTI_AGENT_RESEARCH_PLAN.md`
- `.codex/agents/*.toml`

Summary:
- Captured user decisions: 6 DOF shell nodes, artificial drilling stiffness, Abaqus-style units and signs, constrained DOF elimination, full-vector reaction recovery, no Phase 1 mesh quality diagnostics, singular diagnostics required, `double`, int64 indexing, S4-to-MITC4 mapping, S4R deferral.
- Added technical dossier documents for numerical conventions, Abaqus subset, verification, results schema, and MITC4 formulation.
- Added ADRs for numerical baseline, boundary/reaction policy, drilling stabilization, S4/S4R policy, singular diagnostics, and technical dossier contracts.

Verification:
- `.codex/agents/*.toml` parsed successfully with Python `tomllib`.
- `python scripts/validate_workspace.py` ran, but reported no configured validation commands.

### 2026-04-21 - Initial architecture and agent setup
Author: Codex

Changed files:
- `docs/PRD.md`
- `docs/ARCHITECTURE.md`
- `docs/ADR.md`
- `AGENTS.md`
- `docs/MULTI_AGENT_RESEARCH_PLAN.md`
- `.codex/agents/fem-literature-researcher.toml`
- `.codex/agents/verification-benchmark-researcher.toml`
- `.codex/agents/mitc4-formulation-researcher.toml`
- `.codex/agents/abaqus-compatibility-researcher.toml`

Summary:
- Established solver architecture direction: runtime polymorphism, Strategy + Template Method, Factory + Registry, adapter boundaries, immutable `Domain`, mutable `AnalysisState`, `DofManager` ownership, step/frame/history results.
- Created first research agents for FEM literature, verification benchmarks, MITC4 formulation, and Abaqus compatibility.

Verification:
- `.codex/agents/*.toml` parsed successfully with Python `tomllib`.
- `python scripts/validate_workspace.py` ran, but reported no configured validation commands.

## Known Blockers
- No reaction-force reference artifact exists yet under `references/`.
- The current initial `quad_01.inp` reference contains `S4R`, `Part/Assembly/Instance`, `*Density`, and `NLGEOM=YES`, so it is not a Phase 1 parser acceptance case as-is.
- `quad_02.inp` is a stored Abaqus `TYPE=S4` reference with matching displacement CSV, but it contains `Part/Assembly/Instance` and `*Density`; Step 1 must define a normalized-input or explicit parser-compatibility path before stored-reference regression.

## Current Risks
- Implementation could start from the `quad_01` reference input without accounting for its unsupported Abaqus features.
- Implementation could treat the old MITC4 kernel as authoritative even though it conflicts with the revised formulation contract.
- Reaction output may be wrong if full-space stiffness/load data is not preserved or reconstructed.
- Large-model support may be weakened if any module narrows ids or sparse indices below int64.