All gates verified. Final check — AGENTS.md rules against the project (commands, gates, protocols) — the quick-reference commands all exist and the rules (PLAN §2/§7/§9 references, phase protocol, No CDN, Debugpy, git gates) accurately describe the project; the reasoning bubble is a pure UI change with no new commands or env vars, so no AGENTS.md change is needed.
**Verification complete — full results:**
- **Verified** (implemented by prior task passes, all in working tree): `createReasoningWrap`/`ensureReasoningWrap` live container (D1), `settleReasoning` fold at the 3 settle sites + not at delta (D2), 320px `.reasoning-body` window + pinned-tail follow (D3), zero persistence change (D4), collapsed restore + shared-page parity with D6 step counts, `styles.css` family treatment + reduced-motion still, mock `REASONING_MIDROUND_TRIGGER` flow, 6-test story suite, phase-158 pin updates
- **Full suite:** `uv run pytest` → **3738 passed, 0 failed** · `uv run pytest --cov=app --cov-report=term-missing` → **TOTAL 99% (>90%)** · `uv run ruff check .` → all checks passed · `uv run pyright` → **0 errors, 0 warnings**
- **E2E in isolation** (DB up; port-8123 collision with an unrelated `undercooked` service → `E2E_APP_PORT=8125`/`E2E_MOCK_PORT=8902`, no live change made): `test_reasoning_bubble.py` **6/6** · `test_thinking_timeline.py` ✓ · `test_thinking_display.py` ✓ · `test_tool_call_compact.py` ✓ · `test_big_read_progress.py` ✓ · `test_turn_progress_loader.py` ✓ · `test_share_chat.py` ✓ · `test_chat_persistence.py` ✓ · `test_smoke.py` ✓ (all exit 0, zero failures)
- **Completion criteria:** all 9 checked against the code + test outcomes — container open/live/nested ✓, stays open past mid-round delta ✓, folds at done ✓, restore + shared collapsed with "3 steps" ✓, plain turn = no container ✓, regression suites green ✓, suite/coverage/lint green ✓, diff scope limited to `frontend/assets/{app.js,shared.js,styles.css}` + `tests/` + `README.md` + phase files (no `app/` — D4) ✓
- **Documentation:** README.md "Thinking" section names the Reasoning bubble accurately (320px window, open-until-settle incl. mid-round deltas, "N steps", byte-identical no-container, collapsed on restore/shared) — verified consistent, no changes needed; AGENTS.md — verified consistent, no changes needed; all `.env.example` vars documented
- **Decisions:** commit + phase-dir move left to the harness (per pass rules — no git index/history commands executed); `undercooked` dev server on port 8123 untouched, E2E used the env port overrides
- **Next pending phase:** none — `161_reasoning_bubble` is the last in `todo/`
Single consolidated commit for four completed, validated phases (77, 78,
79, 80). The pipeline run left all work uncommitted because the harness
commits only with PHASE_COMMIT=1 while child executors are forbidden from
committing; the phases themselves all passed validation and moved to
.agents/phases/complete/.
Phase 77 — navbar view refresh
- router.js dispatches bor:view-refresh on re-show / active re-click /
popstate (gated on wasMounted; first show and boot exempt)
- History / RAG / Sources / Tuning re-fetch on refresh (admin branch);
Chat deliberately excluded (stream survival)
- History "Refresh" button (admin-only, in-flight disable + status line)
- New story suite tests/e2e/test_navbar_refresh.py (7 tests)
Phase 78 — static background
- Removed the animated glow layers; static 44px grid over the flat --bg
canvas; default and reduced-motion renders byte-identical
- Updated background/theme E2E suites; removed bg-glow test pins
Phase 79 — API tokens
- api_tokens model + migration 0012; hash-only token service
- Admin tokens API + Tokens admin view; POST /api/token-auth;
live-revoking require_user on chat / suggestions / document content
- Frontend token gate with localStorage cache; anonymous E2E suites
migrated to token login
- New story suite tests/e2e/test_api_tokens.py (9 tests)
Phase 80 — history suggestion chips
- last_questions() endpoint with SEED fallback; startNewChat() refetch
- Seed-semantics docs (config.py, .env.example, README)
- Integration state matrix + E2E suite rewritten to the 4 chip states
Also included: phase-76 report artifacts and the repo restore-test-db
skill (previously untracked), scripts/* ruff fixes from phase 77.
Final gate state (phase 80 final pass, covers everything above):
- uv run pytest --cov=app → 1637 passed, 0 failed, app/ coverage 99%
- uv run ruff check . && uv run pyright → clean, 0 errors
- Per-phase story E2E suites green in isolation
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.
Phase 47 (owner permission 2026-08-27, TODO.md L10–11, roadmap R1): the
full Podman quadlet family (.container, .network, .volume, .image,
.pod, .kube, .swap, .os, .endpoint) and .j2 Jinja templates join the
allowed + default A9 import formats, chunked as plain text (owner
decision — no TOML/Jinja-aware splitter). No env configuration needed:
a default import now indexes them.
- app/config.py: _ALLOWED_IMPORT_EXTENSIONS + the default
import_extensions CSV gain the ten names (the original seven first);
the never-widen BOR_IMPORT_EXTENSIONS validator is untouched and
still rejects truly unknown extensions.
- app/rag/chunker.py: ten _FORMAT_CHUNKERS entries -> chunk_text
(HARD_MAX_CHARS 1200 honored, unknown-suffix fallback unchanged);
docstring/comments cite the A9 revision 2026-08-27.
- tests/fixtures/docs/homelab/: quadlet/compose.container (realistic
quadlet TOML, >1500 chars, [Unit]/[Service]/[Container] sections,
RESE-QUADLET-SENTINEL-77aa), quadlet/lan.network,
quadlet/cache.volume, templates/deploy.j2 (for/set/if Jinja
constructs + RESE-JINJA-SENTINEL-33dd). Every suite that seeds the
fixture tree updates its 9 -> 13 document-count constants.
- tests/unit/test_config.py: allowed set carries all seventeen formats,
default CSV + dotted import_extension_set include the ten, the
validator accepts the new names and still rejects unknowns.
- tests/unit/test_chunker.py: dispatch parity with chunk_text for every
new suffix (parametrized), the .container fixture chunks >=2 under
the cap with the sentinel surviving, the .j2 fixture keeps {{ }}
verbatim, the unknown-suffix fallback is unchanged.
- tests/unit/test_importer.py: a default-extensions walk over a temp
tree indexes exactly the ten new files (unknown/hidden/excluded
filtered), the original seven still walk, stem-title fallback holds.
- tests/integration/test_import_quadlet_jinja.py (new): import_sources
over a temp tree with .container/.volume/.j2 -> documents + chunks
rows with stem titles; delta re-import updates only the changed .j2
doc; prune drops the deleted .volume doc with cascade.
- tests/e2e/test_quadlet_jinja_import.py (new, story suite, mock-only,
isolation): GET /api/docs (admin session) lists the four new-format
docs with non-zero chunk counts and stem titles; the Sources table
renders a row + .doc-link per file; the phase-26 modal shows the
.container TOML ([Container] section + sentinel) with stem title and
the container format badge; a RESE-JINJA-SENTINEL-33dd question
FTS-matches the .j2 chunk -> honest-positive (A8: LOW requires zero
FTS hits) — the bubble is not .is-deflected and a source chip names
templates/deploy.j2.
- README.md + .env.example: the extended default format set (A9
revised 2026-08-27, plain-text chunking, narrow-only rule intact).
- .agent/PLAN.md: the A9 revision (owner-locked R1) — A9 row status,
the revision note under the anchors table, and the §5 chunking-policy
+ §11 workflow lines. The only PLAN edit this phase.
Gates: uv run pytest 795 passed; app/ coverage TOTAL 99% (>90%);
ruff check + pyright clean; story E2E 4/4 in isolation (DB up);
regression E2E suites test_import_documents (3) / test_sync_button
(3) / test_git_sources_admin (6) green in isolation.
Also records the 47_quadlet_jinja_import task-file moves (01–03)
todo/ -> complete/.
GFM pipe tables in the shared renderer (TODO.md L6): a table-protection
pass in frontend/assets/markdown.js (fences -> tables -> escape order)
pulls each header+separator+body block out as a placeholder, renders
cells escape-first with the same inline transforms, and reinserts a
semantic <table class="md-table"> inside a horizontal-overflow
.md-table-wrap — so a pipe table in a chat answer, the document
viewer/modal, and the thinking block all render the same semantic
table. Fences win over tables; lone pipes stay text.
- styles.css: .md-table palette rules (PLAN §7.2 tokens, no motion);
min-width: max-content so a WIDE table keeps its natural width and
the wrapper is the real scroller (width:100% alone wrapped the wide
table's cells — proven by the new E2E).
- mock_llm.py: TABLE_TRIGGER ("show me a table") -> byte-stable
TABLE_ANSWER (3-column table, <img onerror> XSS probe line, wide
5-column table), checked before DEFLECT_MODE like SUMMARY_MODE.
- tests/fixtures/docs/homelab/tables.md: 3x3 pipe table + pipe-heavy
fenced block (viewer/fence subject); the shared fixture set grows
8 -> 9 docs, so every suite pinning the count (added/formats/
stat-docs/EXPECTED_ROWS) is updated accordingly.
- tests/e2e/test_markdown_tables.py (new, story suite): chat table
shape + non-deflection, wide-table wrapper scroll (no page
overflow), XSS probe inert, viewer modal table, fence-not-a-table,
lone pipe stays text.
- tests/e2e/test_agent_document_tools.py: fix a pre-existing flake —
the "Calling tool…" label window is ~0.4 s at the mock's 0.1 s
tool-frame pacing, and a polling expect could stride over it
(failed 3 of 5 runs on the committed baseline). The pre-submit
MutationObserver record is the deterministic source of truth; the
racy to_have_text gate is gone.
uv run pytest: 738 passed, app/ coverage 99% (TOTAL unchanged);
ruff + pyright clean; story E2E 6/6 in isolation; regression E2E
suites (chat_rag, document_viewer, document_summaries, smoke) green.
ducoterra