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/44_markdown_tables/00_phase.md

@@ -0,0 +1,39 @@
+# Phase 44 — Markdown tables (chat, viewer, thinking)
+
+**Source:** `TODO.md` L6 — "Certain markdown formatting isn't working - tables for example don't get rendered as tables in the chat response."
+**Story:** `.agents/user_stories/markdown-tables.md`
+**Context:** `frontend/assets/markdown.js` is the shared escape-first renderer (no libs, A11): fence protection → escape → inline transforms (`code`, `**bold**`, `*em*`, h1–h3, lists) → paragraph pass → fence restore. It has **no table support** — GFM pipe tables render as one raw `|`-littered paragraph. The renderer serves the chat answer, the document viewer/modal, and the thinking block, so one change covers all three.
+
+## Objective
+GFM pipe tables render as semantic, styled, XSS-safe `<table>` elements everywhere the shared renderer runs, with a horizontal-overflow guard for wide tables.
+
+## Dependencies
+- `43_thinking_scroll_back` (todo) — sequential only (the thinking block also renders markdown; no shared-file conflict beyond the renderer itself).
+- `08_story_dark_tech_theme` (complete) — the palette tokens `.md-table` must use.
+- `26_document_modal_viewer` / `10_story_document_viewer` (complete) — the second renderer consumer (viewer/modal).
+
+## Tasks
+1. `01_table_renderer_and_styles.md` — table pass in `markdown.js` + `.md-table` CSS.
+2. `02_mock_table_trigger.md` — deterministic table answer (incl. a wide table) in `mock_llm.py`.
+3. `03_tables_e2e_and_commit.md` — unit pins + story E2E suite + regressions + commit.
+
+## Testing & Quality
+- Unit: new `tests/unit/test_markdown_tables.py` — source pins in the house style (regex over `markdown.js` / `styles.css`): the table-protection pass exists and runs **after** the fence pass and **before** the escape pass; cells are escaped + inline-transformed; output carries `class="md-table"`, `<thead>`, `th scope="col"`, and the `.md-table-wrap` wrapper; `styles.css` has the wrapper overflow rule + table borders + reduced-motion-relevant rules. (Behavior is browser-proven by the E2E; unit pins catch silent regressions without a browser — the established frontend pattern.)
+- Coverage: frontend-only — `app/` TOTAL unchanged, >90%.
+- E2E (mandatory, A16): `tests/e2e/test_markdown_tables.py`, run in isolation.
+
+## Completion Criteria
+- [ ] A pipe table in a chat answer renders `<div class="md-table-wrap"><table class="md-table">` with `<thead>`/`<tbody>`, `<th scope="col">` headers, correct cell texts; no raw `|---|` in the bubble.
+- [ ] A wide table scrolls inside its wrapper; the 46rem column does not overflow the page.
+- [ ] XSS-safe (escaped cells), fences win over tables, lone pipes stay text.
+- [ ] The document viewer/modal renders the same table for a fixture document containing one.
+- [ ] `uv run pytest` green; coverage TOTAL unchanged.
+- [ ] `uv run pytest tests/e2e/test_markdown_tables.py -v --no-cov` green in isolation (DB up).
+- [ ] Regression E2E suites green in isolation: `test_chat_rag.py`, `test_document_viewer.py`, `test_document_summaries.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
+- **A11 untouched** — still the local ~90-line renderer, no library, no CDN.
+- **Owner-locked (2026-08-27, roadmap A3):** scope = GFM pipe tables (header + separator + body); links/blockquotes/hr out of scope; alignment colons parsed but rendered left; wide tables get the `overflow-x: auto` wrapper.
+- **A16/A17 honoured** — one story E2E suite, one atomic commit.