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.

.agents/reports/48_nav_rename_sources/48_nav_rename_sources__01_nav_label_swap.a1.md

@@ -0,0 +1,10 @@
+All done. Final report:
+
+**Task 01 complete — nav label swap + pre-existing defect remediation**
+
+- **Swap as specced**: all six pages now render `#nav-sources` → "RAG", `#nav-git-sources` → "Sources"; ids/hrefs/`hidden`/`is-active` byte-identical; `header.js` changed in two comment blocks only.
+- **Gates**: 794 unit+integration passed; ruff clean; pyright 0 errors; `app/` coverage 99%.
+- **All 42 E2E suites run in isolation**: green except 3 label-text assertions (`test_mobile_hamburger_nav` LINK_TEXTS ×2, `test_git_sources_admin` ×1) — exactly task 02's scope, left untouched.
+- **Deviation (rule 8)**: the owner's ad-hoc commit `03bead0` (sync button → Sources page, New chat → chat page only, dark-red rebrand, steering-toggle removal) left 36 unit + ~20 E2E failures. Fixed one real bug: `sources.js` fed `fmtSyncResult(status)` instead of `status.detail` (all counts read 0).
+- **Stale-test updates beyond markup-only scope**: 5 unit files pinned to the new documented architecture; 15 E2E suites updated (rebrand palette pins `#0f0a0a`/`#1a0f0f`/`#2d0a0a`/`#fca5a5`, sync-trigger helpers navigate to `/sources.html`, New-chat presence asserts → chat-page-only, viewport-independent admin probe via `#nav-sources` reveal instead of bar sign-out visibility).
+- **Not done**: no commit (task 03 commits), `.agents/` untouched, task 02 not started.

.agents/reports/48_nav_rename_sources/48_nav_rename_sources__01_nav_label_swap.a1.validate

@@ -0,0 +1,61 @@
+........................................................................ [  9%]
+........................................................................ [ 18%]
+........................................................................ [ 27%]
+........................................................................ [ 36%]
+........................................................................ [ 45%]
+........................................................................ [ 54%]
+........................................................................ [ 63%]
+........................................................................ [ 72%]
+........................................................................ [ 81%]
+........................................................................ [ 90%]
+........................................................................ [ 99%]
+..                                                                       [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            122      0   100%
+app/api/config.py            7      0   100%
+app/api/docs.py             23      0   100%
+app/api/git_sources.py      66      0   100%
+app/api/health.py           10      0   100%
+app/api/steering.py         42      0   100%
+app/api/suggestions.py       8      0   100%
+app/api/sync.py             81      0   100%
+app/config.py               71      0   100%
+app/core/__init__.py         0      0   100%
+app/core/auth.py            20      0   100%
+app/core/caching.py         92      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                 44      0   100%
+app/models.py               60      0   100%
+app/rag/__init__.py          0      0   100%
+app/rag/agent.py            72      0   100%
+app/rag/chunker.py         206      4    98%
+app/rag/git_sources.py      14      0   100%
+app/rag/importer.py        173      3    98%
+app/rag/llm.py             186      0   100%
+app/rag/overview.py         71      0   100%
+app/rag/prompts.py          65      0   100%
+app/rag/retriever.py        94      3    97%
+app/rag/suggestions.py      27      0   100%
+app/rag/summarizer.py       24      0   100%
+app/schemas.py              99      0   100%
+--------------------------------------------
+TOTAL                     1763     12    99%
+coverage gate: app/ 99% (>90%) OK
+All checks passed!
+0 errors, 0 warnings, 0 informations
+validation OK

.agents/reports/48_nav_rename_sources/48_nav_rename_sources__02_existing_test_labels.a1.md

@@ -0,0 +1,19 @@
+All gates green. Task 02 complete.
+
+**Report — Phase 48, Task 02 (existing test labels)**
+
+Implemented:
+- `test_git_sources_admin.py`: `to_have_text("Git sources")` → `"Sources"` + 2 label comments updated
+- `test_mobile_hamburger_nav.py`: `LINK_TEXTS` → `("Chat", "RAG", "Sources", "Tuning")` + 2 comment updates
+- Comments-only drift fixes: `test_shared_header.py` (docstring + section header → "RAG"), `test_nav_consistency.py` (2 comments, phase-35 history kept), `tests/unit/test_shared_header.py` (docstring)
+- Defect fixes in prior work (pre-existing failures): stale `querySelector("#sign-in-link")` unit assertion → `.sign-in-link` class-based toggle; stale viewport-dependent sign-in *visibility* probes in `test_mobile_hamburger_nav.py::_wait_settled_anonymous` and `test_shared_header.py::assert_shared_bar` → attribute-based `wait_for_function` (mirrors the existing admin probe; phase-46 CSS hides the bar copy at ≤640px)
+
+Results (all green):
+- `uv run pytest tests/unit tests/integration -q` → 794 passed; `uv run pytest --cov=app` → TOTAL 99%
+- `uv run ruff check . && uv run pyright` → clean, 0 errors
+- Isolated E2E: `test_git_sources_admin.py` 6 passed, `test_mobile_hamburger_nav.py` 7 passed, `test_shared_header.py` 6, `test_nav_consistency.py` 6, `test_header_consistency.py` 3, `test_sources_midstream_bug.py` 4, `test_smoke.py` 3
+- Grep criterion: only phase-history comments quote "Git sources" ("then"/"shipped as") — none as the current label
+
+Decisions: two comment-only fixes beyond the enumerated list (unit docstring; hamburger docstring line "clicking 'RAG'") — same drift class as work item 3. No commits/moves made (task 03 owns those).
+
+Next pending task: `.agents/phases/todo/48_nav_rename_sources/03_story_e2e_regression_commit.md`

.agents/reports/48_nav_rename_sources/48_nav_rename_sources__02_existing_test_labels.a1.validate

@@ -0,0 +1,61 @@
+........................................................................ [  9%]
+........................................................................ [ 18%]
+........................................................................ [ 27%]
+........................................................................ [ 36%]
+........................................................................ [ 45%]
+........................................................................ [ 54%]
+........................................................................ [ 63%]
+........................................................................ [ 72%]
+........................................................................ [ 81%]
+........................................................................ [ 90%]
+........................................................................ [ 99%]
+..                                                                       [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            122      0   100%
+app/api/config.py            7      0   100%
+app/api/docs.py             23      0   100%
+app/api/git_sources.py      66      0   100%
+app/api/health.py           10      0   100%
+app/api/steering.py         42      0   100%
+app/api/suggestions.py       8      0   100%
+app/api/sync.py             81      0   100%
+app/config.py               71      0   100%
+app/core/__init__.py         0      0   100%
+app/core/auth.py            20      0   100%
+app/core/caching.py         92      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                 44      0   100%
+app/models.py               60      0   100%
+app/rag/__init__.py          0      0   100%
+app/rag/agent.py            72      0   100%
+app/rag/chunker.py         206      4    98%
+app/rag/git_sources.py      14      0   100%
+app/rag/importer.py        173      3    98%
+app/rag/llm.py             186      0   100%
+app/rag/overview.py         71      0   100%
+app/rag/prompts.py          65      0   100%
+app/rag/retriever.py        94      3    97%
+app/rag/suggestions.py      27      0   100%
+app/rag/summarizer.py       24      0   100%
+app/schemas.py              99      0   100%
+--------------------------------------------
+TOTAL                     1763     12    99%
+coverage gate: app/ 99% (>90%) OK
+All checks passed!
+0 errors, 0 warnings, 0 informations
+validation OK

.agents/reports/48_nav_rename_sources/48_nav_rename_sources__03_story_e2e_regression_commit.a1.md

@@ -0,0 +1,10 @@
+**Phase 48 task 03 complete — all gates green, committed as `872a07c`.**
+
+- Implemented `tests/e2e/test_nav_rename_sources.py` (4 tests: admin labels/order/markers on all six pages incl. login redirect-suppression + seeded viewer, click-navigation with `is-active`, anonymous ship-hidden contract, untouched `#sync-label`/`#doc-back` guards)
+- Story E2E in isolation: `uv run pytest tests/e2e/test_nav_rename_sources.py -v --no-cov` → **4 passed**
+- All 8 regression suites green in isolation: nav_consistency 6, shared_header 6, mobile_hamburger_nav 7, git_sources_admin 6, header_consistency 3, sources_midstream_bug 4, smoke 3, tuning_nav_link 4 — none needed further label fixes
+- `uv run pytest --cov=app --cov-report=term-missing` → **794 passed, TOTAL 99%** (>90%, unchanged — frontend-only); `uv run ruff check .` clean; `uv run pyright` → 0 errors
+- UI Structure Check: labeled `<a>`s in `<nav aria-label="Primary">` on all six pages, labels-only change, no CDN (no-CDN integration test green)
+- Decision: staged whole phase files per task; commit body notes the six pages + header.js also carry the owner's same-day in-flight header rework (mobile sign-in copy, sync ship-hidden) already in the tree
+- Committed 17 files (`--no-gpg-sign`): 6 HTML + header.js + 5 test files + story + moved `complete/48_nav_rename_sources`; `todo/` no longer lists 48
+- Next pending: phase **49_archive_upload_sources** (`.agents/phases/todo/`)

.agents/reports/48_nav_rename_sources/48_nav_rename_sources__03_story_e2e_regression_commit.a1.validate

@@ -0,0 +1,61 @@
+........................................................................ [  9%]
+........................................................................ [ 18%]
+........................................................................ [ 27%]
+........................................................................ [ 36%]
+........................................................................ [ 45%]
+........................................................................ [ 54%]
+........................................................................ [ 63%]
+........................................................................ [ 72%]
+........................................................................ [ 81%]
+........................................................................ [ 90%]
+........................................................................ [ 99%]
+..                                                                       [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            122      0   100%
+app/api/config.py            7      0   100%
+app/api/docs.py             23      0   100%
+app/api/git_sources.py      66      0   100%
+app/api/health.py           10      0   100%
+app/api/steering.py         42      0   100%
+app/api/suggestions.py       8      0   100%
+app/api/sync.py             81      0   100%
+app/config.py               71      0   100%
+app/core/__init__.py         0      0   100%
+app/core/auth.py            20      0   100%
+app/core/caching.py         92      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                 44      0   100%
+app/models.py               60      0   100%
+app/rag/__init__.py          0      0   100%
+app/rag/agent.py            72      0   100%
+app/rag/chunker.py         206      4    98%
+app/rag/git_sources.py      14      0   100%
+app/rag/importer.py        173      3    98%
+app/rag/llm.py             186      0   100%
+app/rag/overview.py         71      0   100%
+app/rag/prompts.py          65      0   100%
+app/rag/retriever.py        94      3    97%
+app/rag/suggestions.py      27      0   100%
+app/rag/summarizer.py       24      0   100%
+app/schemas.py              99      0   100%
+--------------------------------------------
+TOTAL                     1763     12    99%
+coverage gate: app/ 99% (>90%) OK
+All checks passed!
+0 errors, 0 warnings, 0 informations
+validation OK