refactor(agents): migrate .agent/ planning tree to .agents/

Standardize on the .agents/ directory (shared with project skills): phases/, user_stories/, reports/, screenshots/, validate.sh, and phase-sessions/ + pipeline.log all move to .agents/ (git mv preserves history; runtime artifacts move alongside). Updates every reference in AGENTS.md, README.md, .gitignore, app docstrings, and test story headers. Historical KB content in data/ and the runtime pipeline.log transcript are left untouched.
2026-09-05 10:57:07 -04:00
parent 766702c750
commit dbf2af26c6
1118 changed files with 664 additions and 664 deletions
@@ -0,0 +1,12 @@
+All completion criteria verified green. Final report:
+
+**Phase 23 — final verification pass: all green, no code defects found**
+- Verified: relative `./header.js` imports in all 4 page scripts; no direct `header.js` script tags in any HTML; Containerfile stage 1 bundles 4 modules + minifies `markdown.js`/`styles.css` + copies all 4 pages; story file + report + logs present
+- `podman build -f Containerfile .` → green (tag `phase23verify`; layers content-cached from the verified build); log excerpt saved to `.agents/reports/23_containerfile_build/final_verification.log`
+- Image smoke (throwaway Postgres 17+pgvector, isolated net, torn down): `/`, `/sources.html`, `/document.html`, `/login.html` → 200; all 6 assets → 200, raw `/assets/header.js` → 404 (bundled); `app.js` minified w/ header code; `cdn_violations=0`, `direct_header_script_tags=0` → SMOKE_PASS
+- `uv run pytest` → 335 passed · `--cov=app` → 335 passed, TOTAL 99% (≥ prior, >90% gate) · `ruff && pyright` → clean
+- E2E isolated: smoke 3 ✓, shared_header 6 ✓, chat_persistence 4 ✓ · integration isolated: containerfile_assets 6/6 ✓
+- Commit `d7a4064` exists with the exact phase message, 0 GPG signature lines
+
+**Notes:** no fixes needed. Two pre-existing unstaged items left untouched by design: task-02 phase-file move (harness-managed) and a new user TODO item in `TODO.md` ("global tuning without a chat") not yet phased.
+**Next pending phase:** `24_whole_document_context`.
@@ -0,0 +1,46 @@
+........................................................................ [ 21%]
+........................................................................ [ 42%]
+........................................................................ [ 64%]
+........................................................................ [ 85%]
+...............................................                          [100%]
+=============================== warnings summary ===============================
+.venv/lib/python3.13/site-packages/fastapi/testclient.py:1
+  /var/home/ducoterra/Projects/Personal/brain_of_reese/.venv/lib/python3.13/site-packages/fastapi/testclient.py:1: StarletteDeprecationWarning: Using `httpx` with `starlette.testclient` is deprecated; install `httpx2` instead.
+    from starlette.testclient import TestClient as TestClient  # noqa
+
+-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
+================================ tests coverage ================================
+_______________ coverage: platform linux, python 3.13.13-final-0 _______________
+
+Name                     Stmts   Miss  Cover
+--------------------------------------------
+app/__init__.py              1      0   100%
+app/api/__init__.py          0      0   100%
+app/api/auth.py             22      0   100%
+app/api/chat.py             95      0   100%
+app/api/docs.py             23      0   100%
+app/api/health.py           10      0   100%
+app/api/steering.py         33      0   100%
+app/api/suggestions.py       8      0   100%
+app/config.py               56      0   100%
+app/core/__init__.py         0      0   100%
+app/core/auth.py            20      0   100%
+app/core/debugging.py       29      2    93%
+app/core/logging.py         13      0   100%
+app/db.py                   21      0   100%
+app/main.py                 36      0   100%
+app/models.py               46      0   100%
+app/rag/__init__.py          0      0   100%
+app/rag/chunker.py         206      4    98%
+app/rag/importer.py        150      5    97%
+app/rag/llm.py             105      0   100%
+app/rag/prompts.py          44      0   100%
+app/rag/retriever.py       102      3    97%
+app/rag/suggestions.py      27      0   100%
+app/schemas.py              62      0   100%
+--------------------------------------------
+TOTAL                     1109     14    99%
+coverage gate: app/ 99% (>90%) OK
+All checks passed!
+0 errors, 0 warnings, 0 informations
+validation OK
@@ -0,0 +1,17 @@
+Task 01 complete — all gates green.
+
+**Implemented**
+- Root cause fixed: `frontend/assets/{app,sources,document,login}.js` now `import … from "./header.js"` (relative, owner-confirmed)
+- Removed the four redundant direct `<script src="/assets/header.js">` tags + updated load-order comments in all four HTML pages (single-evaluation design)
+- `Containerfile` stage 1: global `npm install -g esbuild@0.25.5` (local install left the binary off `RUN`'s PATH — second, previously unrecorded build blocker: `esbuild: not found`) + bundles all 4 page modules, minifies `markdown.js` (no `--bundle`) and `styles.css`, copies all 4 HTML pages
+- Updated 4 phase-19 unit tests in `tests/unit/test_shared_header.py` that pinned the removed tag-based design; now pin the relative-import/no-tag contract
+
+**Verification (exact commands)**
+- `podman build -t brain-of-reese/app:phase23test -f Containerfile .` → exit 0 (before/after logs in `.agents/reports/23_containerfile_build/`)
+- Image smoke vs throwaway pg17+pgvector: all 4 pages + 6 assets → 200; raw `/assets/header.js` → 404; bundles contain header code; 0 CDN refs → `SMOKE_PASS` (teardown done)
+- Dev server: 4 pages 200, 0 header.js tags; `uv run pytest tests/e2e/test_smoke.py -v --no-cov` → 3 passed; `test_shared_header.py` → 6 passed; `test_chat_persistence.py` → 4 passed
+- `uv run pytest --cov=app --cov-report=term-missing` → 329 passed, 99% coverage; `uv run ruff check . && uv run pyright` → clean
+
+**Decisions**: image tag `brain-of-reese/app:phase23test` kept as build evidence; pre-existing uncommitted TODO.md/phase-22-move changes left untouched (task 02's add-list excludes TODO.md).
+
+**Next pending task**: `.agents/phases/todo/23_containerfile_build/02_integration_test_commit.md`
@@ -0,0 +1,46 @@
+........................................................................ [ 21%]
+........................................................................ [ 43%]
+........................................................................ [ 65%]
+........................................................................ [ 87%]
+.........................................                                [100%]
+=============================== warnings summary ===============================
+.venv/lib/python3.13/site-packages/fastapi/testclient.py:1
+  /var/home/ducoterra/Projects/Personal/brain_of_reese/.venv/lib/python3.13/site-packages/fastapi/testclient.py:1: StarletteDeprecationWarning: Using `httpx` with `starlette.testclient` is deprecated; install `httpx2` instead.
+    from starlette.testclient import TestClient as TestClient  # noqa
+
+-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
+================================ tests coverage ================================
+_______________ coverage: platform linux, python 3.13.13-final-0 _______________
+
+Name                     Stmts   Miss  Cover
+--------------------------------------------
+app/__init__.py              1      0   100%
+app/api/__init__.py          0      0   100%
+app/api/auth.py             22      0   100%
+app/api/chat.py             95      0   100%
+app/api/docs.py             23      0   100%
+app/api/health.py           10      0   100%
+app/api/steering.py         33      0   100%
+app/api/suggestions.py       8      0   100%
+app/config.py               56      0   100%
+app/core/__init__.py         0      0   100%
+app/core/auth.py            20      0   100%
+app/core/debugging.py       29      2    93%
+app/core/logging.py         13      0   100%
+app/db.py                   21      0   100%
+app/main.py                 36      0   100%
+app/models.py               46      0   100%
+app/rag/__init__.py          0      0   100%
+app/rag/chunker.py         206      4    98%
+app/rag/importer.py        150      5    97%
+app/rag/llm.py             105      0   100%
+app/rag/prompts.py          44      0   100%
+app/rag/retriever.py       102      3    97%
+app/rag/suggestions.py      27      0   100%
+app/schemas.py              62      0   100%
+--------------------------------------------
+TOTAL                     1109     14    99%
+coverage gate: app/ 99% (>90%) OK
+All checks passed!
+0 errors, 0 warnings, 0 informations
+validation OK
@@ -0,0 +1,11 @@
+Everything is green. Final report:
+
+**Phase 23 · Task 02 — complete**
+
+- **`tests/integration/test_containerfile_assets.py`** (new, hermetic — text-only, no podman/network/DB): 6 pins — stage-1 `cp` set == pages on disk; every local `assets/` src/href has a stage-1 producer; HTML module set == esbuild `--bundle` inputs; no direct `header.js` tag + relative `from "./header.js"` in all four page scripts; `markdown.js` minified without `--bundle` and module-syntax-free in source; concrete `esbuild@X.Y.Z` pin. Mutation-checked: 5 induced regressions each fail the right test(s).
+- **`.agents/user_stories/containerfile-build.md`** (story, repo format, verbatim TODO L6 bug + diagnosis + A4 decisions + test mapping) and **`.agents/reports/23_containerfile_build/phase_report.md`** (build log excerpt, `SMOKE_PASS` evidence, regression/coverage results) written and force-added.
+- **Results:** `uv run pytest` → 335 passed (329→335); `--cov=app` → TOTAL 99% (≥ today's 99%, >90% gate); E2E isolated: `test_smoke.py` 3 passed, `test_shared_header.py` 6 passed, `test_chat_persistence.py` 4 passed (logs in reports dir); `ruff check .` + `pyright` → clean.
+- **Commit:** `d7a4064` `fix(build): Containerfile builds again — relative module imports, all four pages and shared assets in the image` (`--no-gpg-sign`; includes task-01's Containerfile/frontend/test changes + story + report + task-01 file moved to `complete/`).
+- **Notes:** phase-directory move left to the harness (executor rule); `git add -A .agents/` needed `-u` + targeted `-f` (`.agents/` gitignored); pre-existing `TODO.md` mod left uncommitted per task add-list.
+
+**Next pending task:** `.agents/phases/todo/24_whole_document_context/01_remove_context_cap.md`
@@ -0,0 +1,46 @@
+........................................................................ [ 21%]
+........................................................................ [ 42%]
+........................................................................ [ 64%]
+........................................................................ [ 85%]
+...............................................                          [100%]
+=============================== warnings summary ===============================
+.venv/lib/python3.13/site-packages/fastapi/testclient.py:1
+  /var/home/ducoterra/Projects/Personal/brain_of_reese/.venv/lib/python3.13/site-packages/fastapi/testclient.py:1: StarletteDeprecationWarning: Using `httpx` with `starlette.testclient` is deprecated; install `httpx2` instead.
+    from starlette.testclient import TestClient as TestClient  # noqa
+
+-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
+================================ tests coverage ================================
+_______________ coverage: platform linux, python 3.13.13-final-0 _______________
+
+Name                     Stmts   Miss  Cover
+--------------------------------------------
+app/__init__.py              1      0   100%
+app/api/__init__.py          0      0   100%
+app/api/auth.py             22      0   100%
+app/api/chat.py             95      0   100%
+app/api/docs.py             23      0   100%
+app/api/health.py           10      0   100%
+app/api/steering.py         33      0   100%
+app/api/suggestions.py       8      0   100%
+app/config.py               56      0   100%
+app/core/__init__.py         0      0   100%
+app/core/auth.py            20      0   100%
+app/core/debugging.py       29      2    93%
+app/core/logging.py         13      0   100%
+app/db.py                   21      0   100%
+app/main.py                 36      0   100%
+app/models.py               46      0   100%
+app/rag/__init__.py          0      0   100%
+app/rag/chunker.py         206      4    98%
+app/rag/importer.py        150      5    97%
+app/rag/llm.py             105      0   100%
+app/rag/prompts.py          44      0   100%
+app/rag/retriever.py       102      3    97%
+app/rag/suggestions.py      27      0   100%
+app/schemas.py              62      0   100%
+--------------------------------------------
+TOTAL                     1109     14    99%
+coverage gate: app/ 99% (>90%) OK
+All checks passed!
+0 errors, 0 warnings, 0 informations
+validation OK