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/40_tuning_toggle_flash/00_phase.md

@@ -0,0 +1,37 @@
+# Phase 40 — Tuning toggle anonymous flash
+
+**Source:** `TODO.md` L3 — "Loading the page briefly shows the 'Tuning' button in the header even when the user isn't authenticated. Only show that if the user is authenticated."
+**Story:** `.agents/user_stories/tuning-toggle-flash.md`
+**Context:** Phase 15/34 shared header (`frontend/assets/header.js` owns `#steering-toggle` / `#steering-panel` on all six pages; anonymous → `remove()` post-whoami). The admin-only **nav links** already ship `hidden` (phase-19 contract) — the flashing control is the **steering toggle button labeled "Tuning"**, which ships visible in all six pages and is removed only after `/api/whoami` resolves.
+
+## Objective
+Kill the anonymous flash: the tuning toggle ships `hidden` in every page's markup and is revealed only when whoami says admin (the exact ship-hidden / reveal-for-admin contract the nav links use), so an anonymous user never sees the "Tuning" button — not for a single frame.
+
+## Dependencies
+- `39_configurable_brand` (complete; last existing phase) — current header state: full shared bar on all six pages.
+- `19_shared_header` / `16_admin_auth` / `34_consistent_navbar` (complete) — the `fetchIsAdmin()` gate, the ship-hidden nav contract, and the module-owned steering controls this task modifies.
+
+## Tasks
+1. `01_toggle_ships_hidden.md` — add `hidden` to `#steering-toggle` in all six pages and reveal-for-admin in `header.js`; pin at source level.
+2. `02_flash_e2e_and_regression.md` — story E2E suite (never-visible-for-anonymous, admin reveal, nav-contract regression) + regression pass + commit.
+
+## Testing & Quality
+- Unit: new `tests/unit/test_steering_toggle_visibility.py` — `hidden` present on `#steering-toggle` in all six HTML pages; `header.js` unhides for admin (line before `refreshSteering()`) and the anonymous `remove()` path is intact; any existing source-pin test asserting the exact old markup is updated (check `tests/unit/test_shared_header.py`, `test_steering.py`).
+- Coverage: frontend-only — the `app/` >90% gate is unaffected (must stay unchanged).
+- E2E (mandatory, A16): `tests/e2e/test_tuning_toggle_flash.py`, run in isolation.
+
+## Completion Criteria
+- [ ] Anonymous load of every page: the toggle is never visible (MutationObserver records zero visible frames) and is absent from the DOM after load.
+- [ ] Admin load: toggle visible, panel opens, count badge correct — admin behavior unchanged.
+- [ ] `uv run pytest` green; `uv run pytest --cov=app --cov-report=term-missing` TOTAL unchanged.
+- [ ] `uv run pytest tests/e2e/test_tuning_toggle_flash.py -v --no-cov` green in isolation.
+- [ ] Regression E2E suites green in isolation: `test_shared_header.py`, `test_global_tuning.py`, `test_steering.py`, `test_tuning_nav_link.py`, `test_smoke.py`.
+- [ ] `uv run ruff check . && uv run pyright` clean.
+- [ ] UI Structure Check (AGENTS.md rule 5): no new focus targets; landmarks/contrast unchanged; no CDN.
+- [ ] One `--no-gpg-sign` commit; phase dir moved `.agents/phases/todo/` → `.agents/phases/complete/`.
+
+## Locked decisions
+- **A10 untouched** — no API change; the fix is pure UI visibility off the existing `/api/whoami` gate.
+- **A11 untouched** — no new assets, no CDN.
+- **Phase-16 contract preserved** — anonymous still gets "absent, not hidden" (remove-from-DOM); this phase only removes the pre-whoami flash window.
+- **A16/A17 honoured** — one story E2E suite, one atomic commit.