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/phases/complete/42_no_reply_autoscroll/00_phase.md

@@ -0,0 +1,36 @@
+# Phase 42 — No reply autoscroll
+
+**Source:** `TODO.md` L5 — "Get rid of the chat reply autoscroll, it's breaking things like making it impossible for the user to scroll while a reply generates."
+**Story:** `.agents/user_stories/no-reply-autoscroll.md`
+**Context:** Phase 18 ("follow-the-bottom", owner choice 2026-08-23) added `NEAR_BOTTOM_PX = 200` / `isNearBottom()` / `scrollReveal(wrap, behavior, force)` in `frontend/assets/app.js`: the page auto-scrolls on every `thinking` / `tool` / `delta` frame while the user is within 200px of the bottom. The owner now finds that fighting their own scroll. The gate and the per-frame scrolls are **removed**; scrolling happens only on explicit user intent (submit, restore landing).
+
+## Objective
+The chat page never auto-scrolls during a turn. The viewport moves only when the user submits (their message is revealed) or when a persisted conversation is restored (one-shot landing) — both user-initiated.
+
+## Dependencies
+- `41_sync_fail_fast_models` (todo) — sequential execution only (no code overlap).
+- `18_follow_bottom_scroll` (complete) — the code being removed; `14_chat_persistence` (complete) — the restore landing that must survive; `17_thinking_display` / `11_long_answers` (complete) — the thinking window-pin and long-answer behavior this phase must not break.
+
+## Tasks
+1. `01_remove_autofollow.md` — strip the phase-18 gate + per-frame scrolls from `app.js`; rewrite the unit pin for the new contract.
+2. `02_no_autoscroll_e2e_and_commit.md` — replace the phase-18 E2E with the inverse-contract suite + regressions + commit.
+
+## Testing & Quality
+- Unit: `tests/unit/test_frontend_scroll.py` **rewritten** — pins the new contract: no `NEAR_BOTTOM_PX` / `isNearBottom` in `app.js`; the scroll helper scrolls unconditionally (smooth / reduced-motion-aware); the user-submit path scrolls; the thinking/tool/delta handlers contain **no** page-scroll call; the restore landing keeps its one-shot forced scroll.
+- Coverage: frontend-only — `app/` TOTAL unchanged, >90%.
+- E2E (mandatory, A16): `tests/e2e/test_no_reply_autoscroll.py`, run in isolation. `tests/e2e/test_follow_bottom_scroll.py` is **deleted** (behavior intentionally removed by owner direction 2026-08-27).
+
+## Completion Criteria
+- [ ] During thinking / tool / answer streaming, `window.scrollY` is stable (±1px) while the viewport is scrolled up.
+- [ ] Submit still reveals the user's message; reload still lands one-shot on the latest message.
+- [ ] `uv run pytest` green; coverage TOTAL unchanged.
+- [ ] `uv run pytest tests/e2e/test_no_reply_autoscroll.py -v --no-cov` green in isolation (DB up).
+- [ ] Regression E2E suites green in isolation: `test_chat_rag.py`, `test_thinking_display.py`, `test_chat_persistence.py`, `test_long_answers.py`, `test_smoke.py`.
+- [ ] `uv run ruff check . && uv run pyright` clean.
+- [ ] One `--no-gpg-sign` commit; phase dir moved to `.agents/phases/complete/`.
+
+## Locked decisions
+- **Owner direction (2026-08-27, roadmap A1)** revises the phase-18 owner choice (2026-08-23): follow-the-bottom auto-follow is removed; submit-reveal + restore-landing are kept. Recorded in the story file and the `app.js` docstring (PLAN.md §7.4's Scroll row is a PLAN-side revision to be noted by the owner — this phase does not edit PLAN.md).
+- **A15 unchanged** — the SSE contract is untouched; this is pure client-side behavior.
+- **The thinking window's internal pin** (`textEl.scrollTop`, phase 17) is untouched here — phase 43 reworks it separately.
+- **A16/A17 honoured** — one story E2E suite (replacing the removed one), one atomic commit.