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 The old phases/1-linear-static-mitc4 path is historical and superseded after the MITC4 formulation reset.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.