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/42_no_reply_autoscroll/42_no_reply_autoscroll__00_phase.a1.md

@@ -0,0 +1,21 @@
+All criteria verified — no defects found. Final report:
+
+## Phase 42 — No reply autoscroll: final verification pass — GREEN
+
+- Verified (no code changes needed): `app.js` gate removed — no `NEAR_BOTTOM_PX`/`isNearBottom`; `scrollReveal` is the single unconditional (reduced-motion-aware) scroll call; thinking/tool/delta + typing paths are scroll-free; submit-reveal and one-shot restore landing kept; unit pin rewritten; phase-18 E2E deleted, replaced by `test_no_reply_autoscroll.py`.
+- `uv run pytest --cov=app --cov-report=term-missing` → 723 passed; TOTAL 99% (>90%, `app/` untouched by phase commit, so unchanged).
+- `uv run ruff check . && uv run pyright` → All checks passed; 0 errors.
+- `uv run pytest tests/e2e/test_no_reply_autoscroll.py -v --no-cov` (isolated, DB up) → 5/5 passed (78.9s).
+- Regression suites, each isolated: `test_chat_rag` 3/3, `test_thinking_display` 5/5, `test_chat_persistence` 4/4, `test_long_answers` 2/2, `test_smoke` 3/3.
+
+**Completion criteria:**
+1. scrollY stable ±1px during streaming (viewport up) — ✅ (E2E tests 1–2)
+2. Submit reveals message; reload lands one-shot — ✅ (E2E tests 3–4)
+3. pytest green, coverage TOTAL unchanged — ✅ (723 passed, 99%)
+4. Phase E2E green in isolation — ✅
+5. 5 regression E2E suites green in isolation — ✅
+6. ruff + pyright clean — ✅
+7. One `--no-gpg-sign` commit, phase in `complete/` — ✅ (`7c67633 fix(chat): …`, no GPG sig, frontend/tests only; task files in `complete/42_no_reply_autoscroll/`)
+
+- **Deviations:** none. Overview stays in `todo/` for the harness to move. Pre-existing untracked `NOTES.md` left as-is (not part of phase 42).
+- **Next pending phase:** `43_thinking_scroll_back`

.agents/reports/42_no_reply_autoscroll/42_no_reply_autoscroll__00_phase.a1.validate

@@ -0,0 +1,60 @@
+........................................................................ [  9%]
+........................................................................ [ 19%]
+........................................................................ [ 29%]
+........................................................................ [ 39%]
+........................................................................ [ 49%]
+........................................................................ [ 59%]
+........................................................................ [ 69%]
+........................................................................ [ 79%]
+........................................................................ [ 89%]
+........................................................................ [ 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               66      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            81      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                     1767     12    99%
+coverage gate: app/ 99% (>90%) OK
+All checks passed!
+0 errors, 0 warnings, 0 informations
+validation OK

.agents/reports/42_no_reply_autoscroll/42_no_reply_autoscroll__01_remove_autofollow.a1.md

@@ -0,0 +1,19 @@
+Task 01 complete. Report:
+
+**Implemented**
+- `frontend/assets/app.js`: deleted `NEAR_BOTTOM_PX` + `isNearBottom()`; `scrollReveal` is now an unconditional `scrollIntoView({behavior, block:"end"})` (single call in file, no `force`); `addMessage(who, html, scroll=false)` — submit passes `true` (reveal kept), restore landing passes `true` (one-shot kept), brain bubbles/typing never scroll; thinking/tool/delta branches dropped their `scrollReveal` calls (thinking block keeps its internal `textEl.scrollTop` pin — phase 17); docstrings updated to the phase-42 contract.
+- `tests/unit/test_frontend_scroll.py`: rewritten — 9 pins for the new contract (gate absent, helper unconditional, explicit scroll intent, streaming handlers scroll-free, restore one-shot, reduced-motion `SCROLL` intact, preventScroll focus-back).
+- `tests/unit/test_chat_persistence.py`: restore pin updated from old `"auto", true` signature to `true` (direct consequence of the new `addMessage` signature).
+
+**Test / lint / coverage**
+- `uv run pytest --cov=app --cov-report=term-missing` → 723 passed, app/ TOTAL **99%** (unchanged; no `app/` code touched)
+- `uv run ruff check .` → All checks passed
+- `uv run pyright` → 0 errors, 0 warnings
+- JS syntax verified via `node --check` (ES module)
+
+**Decisions**
+- New `addMessage` has no per-call behavior override, so the restore landing rides default `SCROLL` (smooth) instead of old forced `"auto"` — the task-sanctioned option, noted in the call-site comment.
+- Kept `block: "end"` on the single `scrollIntoView` to preserve reveal/landing semantics.
+- `tests/e2e/test_follow_bottom_scroll.py` left in place — replaced/deleted by task 02.
+
+**Next pending task:** `42_no_reply_autoscroll/02_no_autoscroll_e2e_and_commit.md`

.agents/reports/42_no_reply_autoscroll/42_no_reply_autoscroll__01_remove_autofollow.a1.validate

@@ -0,0 +1,60 @@
+........................................................................ [  9%]
+........................................................................ [ 19%]
+........................................................................ [ 29%]
+........................................................................ [ 39%]
+........................................................................ [ 49%]
+........................................................................ [ 59%]
+........................................................................ [ 69%]
+........................................................................ [ 79%]
+........................................................................ [ 89%]
+........................................................................ [ 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               66      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            81      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                     1767     12    99%
+coverage gate: app/ 99% (>90%) OK
+All checks passed!
+0 errors, 0 warnings, 0 informations
+validation OK

.agents/reports/42_no_reply_autoscroll/42_no_reply_autoscroll__02_no_autoscroll_e2e_and_commit.a1.md

@@ -0,0 +1,10 @@
+Done. Commit `7c67633` landed; repo is functional (only pending items are the harness-managed `.agents` task-file moves and the owner's untracked `NOTES.md`, both left untouched per protocol).
+
+**Report**
+- **Implemented:** `tests/e2e/test_no_reply_autoscroll.py` (5 tests: no autoscroll during long answer with ≥10 samples at 1px tolerance incl. post-`done`; no autoscroll during the ~4.5s thinking stream; submit-from-top reveals the user message via JS send so Playwright's fill auto-scroll can't pre-move the viewport; one-shot restore landing that lands and stays; long answer + sources and collapsed thinking block persist/restore). Deleted `tests/e2e/test_follow_bottom_scroll.py`. Task 01's `app.js` + unit-pin changes (already in working tree) were verified and committed together.
+- **E2E (isolation, DB up):** `uv run pytest tests/e2e/test_no_reply_autoscroll.py -v --no-cov` → **5 passed** (79s). Regressions: `test_chat_rag` 3/3, `test_thinking_display` 5/5, `test_chat_persistence` 4/4, `test_long_answers` 2/2, `test_smoke` 3/3.
+- **Unit+integration:** `uv run pytest --cov=app --cov-report=term-missing` → **723 passed**, TOTAL **99%** (unchanged, >90%).
+- **Lint/types:** `uv run ruff check .` clean; `uv run pyright` → 0 errors.
+- **Commit:** one atomic `--no-gpg-sign` Conventional Commit `fix(chat): stop autoscrolling while a reply streams (owner direction)` — 5 code files; `.agents/` moves stay harness-managed (matches phase-41 precedent).
+- **Notable:** restore-landing asserts latest bubble in lower viewport half (not exact bottom) because source chips append after the smooth scroll call; "last brain bubble" predicates guard `min_bubbles=2` so a second turn's pre-delta window can't match turn 1's bubble.
+- **Next pending task:** none in `todo/42_no_reply_autoscroll/` (task 02 was the last); the harness will move it to `complete/`.

.agents/reports/42_no_reply_autoscroll/42_no_reply_autoscroll__02_no_autoscroll_e2e_and_commit.a1.validate

@@ -0,0 +1,60 @@
+........................................................................ [  9%]
+........................................................................ [ 19%]
+........................................................................ [ 29%]
+........................................................................ [ 39%]
+........................................................................ [ 49%]
+........................................................................ [ 59%]
+........................................................................ [ 69%]
+........................................................................ [ 79%]
+........................................................................ [ 89%]
+........................................................................ [ 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               66      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            81      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                     1767     12    99%
+coverage gate: app/ 99% (>90%) OK
+All checks passed!
+0 errors, 0 warnings, 0 informations
+validation OK