# 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`. Steps 0 through 14 are complete. `quad_02_phase1.inp` is now the normalized Phase 1-compatible input path for the stored `quad_02` S4 reference pair, while the original `quad_02.inp` remains preserved unsupported provenance. Core numeric aliases, DOF mapping, validation harness, model diagnostic context, the Phase 1 parser/domain subset, validation/singular diagnostics, DofManager/reaction foundation, minimum result model metadata, displacement CSV comparator foundation, MITC4 geometry/director scaffolding, MITC4 displacement/strain/tying row scaffolding, MITC4 material/transform/integration scaffolding, MITC4 stiffness/drilling/internal-force scaffolding, MITC4 patch/locking-sensitivity tests, full-space assembly, reduced projection, sparse-pattern scaffold, solver adapter injection, full-vector internal/reaction force state, active AnalysisModel construction, input-to-AnalysisState-to-U/RF result workflow, and the first stored Abaqus displacement regression have been revalidated. The old `phases/1-linear-static-mitc4` path is historical and superseded after the MITC4 formulation reset.

## Completed Work

### 2026-05-04 - P1R-14 stored reference regression completed
Author: Codex

Changed files:
- `tests/test_main.cpp`
- `docs/VERIFICATION_PLAN.md`
- `references/quad_02_notes.md`
- `phases/1-linear-static-mitc4-rebaseline/index.json`
- `PLAN.md`
- `PROGRESS.md`

Summary:
- Added a fixture discovery test that keeps `references/quad_02.inp` as unsupported Abaqus/CAE provenance while verifying `references/quad_02_phase1.inp` is the accepted executable Phase 1 derivative.
- Added the first automated stored Abaqus displacement regression: run `quad_02_phase1.inp`, extract FESA `/results/steps/Step-1/frames/0/fieldOutputs/U`, and compare against `references/quad_02_displacements.csv` by node id.
- Used the documented tolerance for this reference pair: `abs_tol = 1.0e-12`, `rel_tol = 1.0e-5`, `reference_scale = 1.0`.
- Updated verification/reference notes so `quad_02_phase1` is no longer a future regression target; it is now active test coverage.

Verification:
- `python scripts/validate_workspace.py` configured CMake, built `fesa_core` and `fesa_tests`, and ran CTest successfully.
- CTest result: 1 test executable passed.
- Stored reference result: `quad_02_phase1.inp` displacement regression passed against `quad_02_displacements.csv` using the tolerance above.

Follow-up:
- Continue with P1R-15 independent evaluator closeout.
- R-013 remains open: Phase 1 still needs enough additional stored Abaqus S4 reference cases for the PRD target of three stored references: one single-element case, one simple multi-element plate/shell case, and one curved shell benchmark.
- R-010 remains open: no `quad_02_reactions.csv` or other Abaqus reaction CSV exists yet, so `RF` remains verified by internal full-vector equilibrium.

### 2026-05-04 - P1R-13 linear static workflow completed
Author: Codex

Changed files:
- `include/fesa/fesa.hpp`
- `tests/test_main.cpp`
- `phases/1-linear-static-mitc4-rebaseline/index.json`
- `PLAN.md`
- `PROGRESS.md`

Summary:
- Added an explicit `AnalysisModel` value object for the active Phase 1 linear static step, including active element ids, boundary/load indices, shell section indices, and material keys.
- Added `buildLinearStaticAnalysisModel()` and routed `LinearStaticAnalysis` through it before DOF mapping, assembly, solve, state update, and result writing.
- Preserved the one-step Phase 1 execution boundary with a diagnostic for multiple parsed steps instead of silently executing them.
- Added `runLinearStaticInputString()` so parser diagnostics, domain validation diagnostics, active model construction, solve, `AnalysisState`, and `U`/`RF` result writing are exercised as one workflow.
- Extended the in-memory result model with element type metadata and ensured result writing uses the active model step name.
- Added tests for active model activation without mutating `Domain`, multiple-step rejection, input-to-result `U`/`RF` schema readiness, full-vector reaction balance, and parse/validation error propagation through the workflow.

Verification:
- First ran `python scripts/validate_workspace.py` after adding Step 13 tests; it failed as expected because `AnalysisModel` and input-string workflow APIs did not exist yet.
- After implementation, `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:
- Continue with P1R-14 stored-reference displacement regression using `references/quad_02_phase1.inp` and `references/quad_02_displacements.csv`.
- Step 13 intentionally did not add nonlinear, dynamic, pressure, thermal, HDF5, multi-step execution, or stored Abaqus CSV regression behavior.

### 2026-05-04 - P1R-12 assembly sparse solver path completed
Author: Codex

Changed files:
- `include/fesa/fesa.hpp`
- `tests/test_main.cpp`
- `phases/1-linear-static-mitc4-rebaseline/index.json`
- `PLAN.md`
- `PROGRESS.md`

Summary:
- Added deterministic reduced sparse-pattern scaffolding from `DofManager` element equation connectivity, preserving int64 equation and nonzero counts for the future sparse/MKL path.
- Added `projectToReducedSystem()` so constrained/free projection is a named assembly boundary instead of being embedded directly inside `LinearStaticAnalysis`.
- Extended `AssemblyResult` to carry full-space stiffness, full external load, reduced sparse pattern, and diagnostics.
- Reworked assembly to call the rebuilt MITC4 stiffness result path directly and preserve full-space `K_full`/`F_full` for reaction recovery.
- Added solver injection to `LinearStaticAnalysis` so the deterministic Gaussian solver remains the default test adapter while future MKL-backed solvers stay behind the `LinearSolver` interface.
- Added `AnalysisState::f_internal_full` and verified `RF = Fint_full - Fext_full = K_full * U_full - F_full`.
- Added tests for deterministic sparse pattern ordering, reduced projection with known displacement, full-space assembly/load preservation, reduced residual satisfaction, solver adapter injection, and singular solver diagnostic propagation.

Verification:
- First ran `python scripts/validate_workspace.py` after adding Step 12 tests; it failed as expected because reduced sparse pattern, projection, solver injection, and `f_internal_full` did not exist yet.
- After implementation, `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:
- Continue with P1R-13 linear static workflow revalidation from Phase 1 input through `U` and `RF` result fields.
- Step 12 intentionally did not add MKL/TBB APIs, stored Abaqus reference comparison, pressure loads, or a production sparse matrix storage backend.

### 2026-05-04 - P1R-11 MITC4 patch and benchmark tests completed
Author: Codex

Changed files:
- `tests/test_main.cpp`
- `docs/VERIFICATION_PLAN.md`
- `phases/1-linear-static-mitc4-rebaseline/index.json`
- `PLAN.md`
- `PROGRESS.md`

Summary:
- Added reusable MITC4 test helpers for analytic displacement/rotation fields, local strain sampling through the tied strain-row path, and a one-element cantilever smoke model.
- Added constant membrane patch tests that verify uniform local `[eps11, eps22, gamma12]` at all `2 x 2 x 2` samples and positive physical energy.
- Added pure bending, pure transverse shear, and pure twist patch tests to exercise through-thickness bending behavior, MITC transverse shear tying, and bilinear twist/shear interpolation.
- Added a drilling-sensitivity negative check proving membrane patch energy is not hidden by the artificial drilling scale when no drilling DOF participates.
- Added a thin one-element cantilever strip test that verifies tip displacement grows materially as thickness decreases, providing early shear-locking sensitivity coverage before stored Abaqus reference regression.
- Documented the Step 11 analytic patch layer and kept Scordelis-Lo as a deferred benchmark scaffold until pressure-load support and a stored curved-shell reference artifact are defined.

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:
- Continue with P1R-12 assembly, solver-adapter boundary, constrained solve, and full-vector RF recovery revalidation.
- Step 11 intentionally did not execute Abaqus, add pressure loads, add stored CSV reference regression, or tune benchmark tolerances against Abaqus artifacts.

### 2026-05-04 - P1R-10 MITC4 stiffness and drilling completed
Author: Codex

Changed files:
- `include/fesa/fesa.hpp`
- `tests/test_main.cpp`
- `phases/1-linear-static-mitc4-rebaseline/index.json`
- `PLAN.md`
- `PROGRESS.md`

Summary:
- Added tests and implementation for MITC4 element stiffness accumulation using tied strain rows, transformed material matrices, and `2 x 2 x 2` integration samples.
- Added a stiffness result API that exposes local physical stiffness, local drilling-stabilized stiffness, global stiffness, integration-point count, drilling reference diagonal, and drilling stiffness metadata.
- Replaced the old default drilling scale with the documented `drilling_stiffness_scale = 1.0e-3` and applied it to the minimum positive physical local stiffness diagonal before global transformation.
- Added diagnostics for invalid drilling scale and missing positive drilling reference diagonal.
- Added tests for stiffness symmetry, drilling scale sensitivity, rigid translation zero energy, documented drilling-only energy, and `f_int_e = K_e u_e` consistency.
- Routed `MITC4ElementKernel::stiffness` through the rebuilt formulation path so later assembly uses the Step 7 through Step 10 MITC4 helpers.

Verification:
- First ran `python scripts/validate_workspace.py` after adding Step 10 tests; it failed as expected because the MITC4 stiffness/drilling/internal-force APIs did not exist yet.
- After implementation, `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:
- Continue with P1R-11 MITC4 patch, locking-sensitivity, and benchmark tests.
- Step 10 intentionally did not tune the drilling scale to a reference case, add stress/resultant output, introduce reduced integration/hourglass logic, or rebuild sparse/global assembly beyond routing the existing kernel to the new element formulation.

### 2026-05-04 - P1R-09 MITC4 material integration scaffolding completed
Author: Codex

Changed files:
- `include/fesa/fesa.hpp`
- `tests/test_main.cpp`
- `phases/1-linear-static-mitc4-rebaseline/index.json`
- `PLAN.md`
- `PROGRESS.md`

Summary:
- Added tests and implementation for the documented isotropic local plane-stress shell material matrix in strain order `[eps11, eps22, eps33, gamma23, gamma13, gamma12]`, with `sigma_33 = 0` and transverse shear correction `kappa = 5/6`.
- Added material diagnostics for invalid elastic modulus, Poisson ratio, and shear correction factor.
- Added `2 x 2 x 2` Gauss integration point infrastructure with unit weights and total natural-domain weight `8`.
- Added covariant-to-local strain transformation and `D_convected = T^T D_hat T`, including identity and flat-element energy-equivalence tests.
- Added MITC4 material integration sample scaffolding that carries integration basis, tied strain rows, local material, strain transform, and convected material for the later stiffness rebuild.

Verification:
- First ran `python scripts/validate_workspace.py` after adding Step 9 tests; it failed as expected because the MITC4 material/integration APIs did not exist yet.
- After implementation, `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:
- Continue with P1R-10 MITC4 stiffness/internal force rebuild, six-DOF local-to-global transform, and drilling stabilization.
- The legacy `MITC4ElementKernel::stiffness` path still needs to be rebuilt against the Step 7 through Step 9 formulation helpers; Step 9 intentionally did not add reduced integration, hourglass logic, stress/result output recovery, or the final drilling stiffness policy.

### 2026-05-04 - P1R-08 MITC4 covariant strain tying completed
Author: Codex

Changed files:
- `include/fesa/fesa.hpp`
- `tests/test_main.cpp`
- `phases/1-linear-static-mitc4-rebaseline/index.json`
- `PLAN.md`
- `PROGRESS.md`

Summary:
- Added MITC4 tests for global rotation to local `alpha`, `beta`, `gamma` mapping and verified drilling `gamma` does not enter the physical director increment.
- Added degenerated-continuum displacement interpolation tests at the midsurface and through-thickness points, including rotation-driven `q_k = -V2_k alpha_k + V1_k beta_k` behavior.
- Added direct covariant strain-row finite-difference tests in the documented order `[eps11, eps22, eps33, gamma23, gamma13, gamma12]`.
- Added MITC tying tests proving FESA `A/C` signs for `gamma13` and `B/D` signs for `gamma23`, and proving Gauss-point shear rows are interpolated from tying rows rather than using direct Gauss-point transverse shear.
- Implemented reusable MITC4 displacement derivative, direct strain evaluation, direct strain-row, tied strain-row, and row-evaluation helpers for later material/integration and stiffness steps.

Verification:
- First ran `python scripts/validate_workspace.py` after adding Step 8 tests; it failed as expected because the MITC4 displacement/strain/tying APIs did not exist yet.
- After implementation, `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:
- Continue with P1R-09 material matrix, transform, and `2 x 2 x 2` integration scaffolding.
- The existing stiffness kernel still needs to be rebuilt against the new row APIs in steps 9 and 10; Step 8 intentionally did not integrate stiffness, add material transforms, or add S4R behavior.

### 2026-05-04 - P1R-07 MITC4 geometry and directors completed
Author: Codex

Changed files:
- `include/fesa/fesa.hpp`
- `tests/test_main.cpp`
- `phases/1-linear-static-mitc4-rebaseline/index.json`
- `PLAN.md`
- `PROGRESS.md`

Summary:
- Added MITC4 tests for shape-function derivatives, FESA/Abaqus S4 natural-coordinate node order, tying point labels `A`, `B`, `C`, and `D`, and edge-node mapping.
- Added Phase 1 MITC4 geometry structures for natural points, tying points, center midsurface derivatives, center-normal director policy, nodal director frames, and integration-point local Cartesian bases.
- Implemented the documented center director policy `Vn = normalize(G1_c x G2_c)`, nodal `V1 = normalize(EY x Vn)` with deterministic fallback axes, and right-handed `V2 = Vn x V1`.
- Added integration-basis construction from degenerated-continuum covariant basis vectors and diagnostics for invalid thickness, singular center normal, singular basis, and near-zero Jacobian.
- Replaced the legacy `computeLocalBasis()` internals with the new center-director geometry policy while leaving stiffness/strain/drilling reimplementation to later steps.

Verification:
- First ran `python scripts/validate_workspace.py` after adding Step 7 tests; it failed as expected because the MITC4 geometry/director API did not exist yet.
- After implementation, `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:
- Continue with P1R-08 degenerated-continuum displacement, covariant strain rows, and MITC shear tying.
- The existing stiffness kernel still needs to be rebuilt against the new formulation in steps 8 through 10; Step 7 intentionally did not add stiffness, stress, strain, or S4R behavior.

### 2026-05-04 - P1R-06 results model and displacement CSV comparator completed
Author: Codex

Changed files:
- `include/fesa/fesa.hpp`
- `tests/test_main.cpp`
- `docs/RESULTS_SCHEMA.md`
- `docs/VERIFICATION_PLAN.md`
- `phases/1-linear-static-mitc4-rebaseline/index.json`
- `PLAN.md`
- `PROGRESS.md`

Summary:
- Added result model tests for Phase 1 root metadata, frame `0` metadata, and mandatory `U`/`RF` field labels, positions, entity type, and global basis.
- Extended the in-memory result model with solver/schema metadata, linear-static frame metadata, nodal field metadata, and mandatory `U`/`RF` descriptions while keeping `S`, `E`, and `SF` optional.
- Added string/stream-based Abaqus displacement CSV loading so tests can cover required headers, duplicate node labels, missing/non-numeric node labels, and nonnumeric component values without temporary files.
- Strengthened displacement comparison so it matches by node id, verifies exact FESA `U` component labels and nodal/global metadata, rejects duplicate actual node ids, reports missing FESA nodes, and uses combined absolute/relative tolerances.

Verification:
- First ran `python scripts/validate_workspace.py` after adding Step 6 tests; it failed as expected because the result metadata fields and string CSV loader did not exist yet.
- After implementation, `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:
- Continue with P1R-07 MITC4 geometry, node order, tying points, directors, and local bases.
- Keep RF reference CSV availability open; current RF verification remains internal full-vector equilibrium until a stored `*_reactions.csv` artifact is provided.

### 2026-05-04 - P1R-05 DofManager and reaction foundation completed
Author: Codex

Changed files:
- `include/fesa/fesa.hpp`
- `tests/test_main.cpp`
- `phases/1-linear-static-mitc4-rebaseline/index.json`
- `PLAN.md`
- `PROGRESS.md`

Summary:
- Added DofManager tests for six-DOF global ordering, noncontiguous node-id stability, constrained/free partitioning, equation numbering, full-vector reduction/reconstruction, element sparse-connectivity inputs, and a full-system reaction recovery formula.
- Extended `DofManager` with full DOF addresses, constrained full-index lists, full-vector reduction, element full-index connectivity, and element equation-id connectivity while keeping equation ids outside `Node` and `Element`.
- Added `recoverFullReaction(K_full, U_full, F_full)` and routed `LinearStaticAnalysis` through it so reaction recovery remains a full-vector operation rather than a reduced-vector shortcut.
- Updated assembly to consume element full DOF indices from `DofManager`, preserving DofManager ownership of sparse-pattern inputs.

Verification:
- First ran `python scripts/validate_workspace.py` after adding tests; it failed as expected because the new DofManager/reaction APIs did not exist yet.
- After implementing the DofManager and reaction-foundation APIs, `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:
- Continue with P1R-06 results model and displacement CSV comparator foundation.
- Keep RF reference CSV availability open; current RF verification remains internal full-vector equilibrium until a stored `*_reactions.csv` artifact is provided.

### 2026-05-04 - P1R-04 validation and singular diagnostics completed
Author: Codex

Changed files:
- `include/fesa/fesa.hpp`
- `tests/test_main.cpp`
- `phases/1-linear-static-mitc4-rebaseline/index.json`
- `PLAN.md`
- `PROGRESS.md`

Summary:
- Added negative validation tests for missing node/property/material references, missing shell-section/boundary/load sets, missing set members, non-positive shell thickness, invalid boundary/load DOFs, no active elements, no free DOFs, isolated free DOFs, and weak drilling DOF smoke coverage.
- Strengthened `validateDomain` so it reports missing `Nset` node members, missing `Elset` element members, non-positive or non-finite shell thickness, invalid Abaqus DOF ranges, no-free-DOF states, free DOFs untouched by active element connectivity, and free drilling DOF weak-stabilization warnings.
- Kept mesh quality diagnostics out of Phase 1; no aspect ratio, skew, warpage, or distortion diagnostics were added.
- Added keyword context to solver size, solver singularity, and fallback no-free-DOF diagnostics.

Verification:
- First ran `python scripts/validate_workspace.py` after adding tests; it failed as expected on the missing new diagnostics.
- After implementing the validation diagnostics, `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:
- Continue with P1R-05 DofManager and reaction-foundation revalidation.
- Keep RF reference CSV availability open; current Phase 1 RF validation remains internal full-vector equilibrium until a stored `*_reactions.csv` artifact is provided.

### 2026-05-04 - P1R-03 parser/domain subset completed
Author: Codex

Changed files:
- `include/fesa/fesa.hpp`
- `tests/test_main.cpp`
- `docs/ABAQUS_INPUT_SUBSET.md`
- `phases/1-linear-static-mitc4-rebaseline/index.json`
- `PLAN.md`
- `PROGRESS.md`

Summary:
- Added parser acceptance coverage for repeated explicit sets, generated `*Nset` and `*Elset`, `D` exponent numeric input, keyword-line continuation, and every Phase 1 structural input keyword.
- Expanded unsupported-feature coverage for `S4R`, `Part`, `Assembly`, `Instance`, `*Include`, `*Density`, and `NLGEOM=YES`.
- Added negative coverage for unsupported parameters and flags on otherwise supported keywords, unsupported shell-section data modes, malformed numeric fields, and invalid DOF fields with file, line, and keyword diagnostics.
- Tightened the parser so supported keywords reject unknown parameters/flags, fixed-width data rows reject extra non-empty fields, generated sets require exactly `first,last,increment`, and keyword continuation lines are assembled before keyword parsing.
- Clarified `docs/ABAQUS_INPUT_SUBSET.md` so the strict parameter and fixed-width data-row rules are explicit.

Verification:
- First ran `python scripts/validate_workspace.py` after adding unsupported-parameter tests; it failed as expected because the parser still accepted supported keywords with unknown controls.
- After implementing strict keyword-control rejection, validation passed.
- Added keyword-continuation tests and first observed the expected failure; after implementing continuation handling, `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:
- Continue with P1R-04 validation and singular diagnostic coverage.
- Keep `Part/Assembly/Instance`, `S4R`, `*Density`, and `NLGEOM=YES` outside the Phase 1 parser until an ADR and parser contract intentionally broaden the subset.

### 2026-05-04 - P1R-02 core harness guardrails completed
Author: Codex

Changed files:
- `include/fesa/fesa.hpp`
- `tests/test_main.cpp`
- `phases/1-linear-static-mitc4-rebaseline/index.json`
- `PLAN.md`
- `PROGRESS.md`

Summary:
- Strengthened C++ guardrail tests for centralized numeric aliases: `Real`, `GlobalId`, `LocalIndex`, `EquationId`, and `SparseIndex`.
- Expanded DOF mapping coverage to prove all six shell DOFs round-trip with Abaqus DOF numbers `1..6`, labels, and invalid DOF rejection.
- Added compile-time type checks so the core aliases remain `double` and signed `std::int64_t`.
- Added model-validation diagnostic context through a shared `makeDiagnostic` helper and populated source keywords for element, shell section, boundary, cload, analysis model, and missing target diagnostics.
- Kept the existing CMake/CTest validation path as the real repository validation command.

Verification:
- First ran `python scripts/validate_workspace.py` after adding tests; it failed as expected because model diagnostics did not yet populate source keywords.
- After implementing the diagnostic guardrail, `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:
- Continue with P1R-03 parser/domain subset revalidation.
- Leave MITC4 stiffness and parser feature expansion to later dedicated steps.

### 2026-05-04 - P1R-01 quad_02 reference onboarding completed
Author: Codex

Changed files:
- `references/quad_02_phase1.inp`
- `references/quad_02_notes.md`
- `references/README.md`
- `docs/ABAQUS_INPUT_SUBSET.md`
- `docs/VERIFICATION_PLAN.md`
- `tests/test_main.cpp`
- `phases/1-linear-static-mitc4-rebaseline/index.json`
- `PLAN.md`
- `PROGRESS.md`

Summary:
- Preserved `references/quad_02.inp` and `references/quad_02_displacements.csv` unchanged as the original Abaqus/CAE S4 reference provenance.
- Added `references/quad_02_phase1.inp`, a normalized Phase 1-compatible derivative input that removes `Part/Assembly/Instance`, `*Density`, restart/output requests, and unsupported step metadata while preserving ids, connectivity, material, shell thickness, fixed boundary nodes, load node, and load magnitude.
- Added `references/quad_02_notes.md` with provenance, compatibility, unit-system, result mapping, tolerance, and RF limitation notes.
- Added tests proving the original `quad_02.inp` remains unsupported provenance, the normalized input parses into 121 nodes and 100 S4 elements, and `quad_02_displacements.csv` loads 121 node rows.
- Updated reference and parser documentation so the normalized file is the accepted `quad_02` path for future Phase 1 stored-reference regression.

Verification:
- First ran `python scripts/validate_workspace.py` after adding tests; it failed as expected because `quad_02_phase1.inp` did not exist yet.
- After adding the normalized input and documentation, `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:
- Continue with P1R-02 core harness guardrails.
- Keep `RF` verified by internal full-vector equilibrium until a `*_reactions.csv` artifact is provided.

### 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.

## 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.
- Future work could accidentally parse the original `quad_02.inp` instead of the normalized `quad_02_phase1.inp` before parser compatibility is explicitly expanded.
- 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.