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.
This commit is contained in:
2026-09-05 10:57:07 -04:00
parent 766702c750
commit dbf2af26c6
1118 changed files with 664 additions and 664 deletions
@@ -0,0 +1,20 @@
All criteria verified green; no defects found, no fixes needed.
## Phase 70 — Harness-Aligned Tools: verification report
**Verified (final pass — all 5 tasks already complete in `complete/`):**
- `AGENT_TOOLS` = exactly `ls`(path?) / `read`(path) / `grep`(pattern, path?); `rg "list_documents|read_document|search_documents" app/` → no matches
- `read` splits combined `source/path` at first slash, full content (A7); `grep` locked A5 (fixed substring, case-insens., 20×200, locator-only); `ls` prints `source: X | path: Y | title: Z`
- SSE `tool` frames: new names; `argument` = the single string passed (`grep`→pattern, else path) or null
- Kill switch (`MAX_ROUNDS=0` → one `tools=None` request) and LOW/deflected byte-identity pinned by unit tests and green
- `TOOLS_SECTION` rewritten for the new surface; frontend `read`/`grep`/`ls` render (old names still render for persisted chats); README §"Agent document tools (ls + read + grep)" updated
**Gates (exact commands):**
- `uv run pytest --cov=app` → exit 0, all pass; TOTAL coverage **99%** (>90%)
- `uv run ruff check . && uv run pyright` → "All checks passed!" / "0 errors"
- `uv run pytest tests/e2e/test_harness_aligned_tools.py -v --no-cov` → **3 passed** (ls→read, grep→read, wire-argument rule)
- Isolated regressions: `test_agent_document_tools` **4 passed**, `test_agent_unlimited_tools` **4 passed**, `test_search_tool` **3 passed**, `test_chat_rag` **3 passed**
- Commit `801639e` exists with the exact Commit-block message; phase dir in `.agents/phases/complete/`
**Deviations:** none — no code changes required this pass.
**Next pending phase:** `71_scaffolding_guardrails` (in `todo/`).
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=============================== 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 149 0 100%
app/api/chats.py 110 0 100%
app/api/config.py 7 0 100%
app/api/doc_drafts.py 93 0 100%
app/api/docs.py 50 0 100%
app/api/git_sources.py 212 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 101 0 100%
app/config.py 126 0 100%
app/core/__init__.py 0 0 100%
app/core/auth.py 20 0 100%
app/core/caching.py 108 0 100%
app/core/debugging.py 29 2 93%
app/core/docs_push.py 39 0 100%
app/core/logging.py 13 0 100%
app/db.py 21 0 100%
app/main.py 52 0 100%
app/models.py 86 0 100%
app/rag/__init__.py 0 0 100%
app/rag/agent.py 139 0 100%
app/rag/archive_upload.py 128 0 100%
app/rag/chunker.py 206 4 98%
app/rag/git_sources.py 14 0 100%
app/rag/importer.py 180 3 98%
app/rag/llm.py 213 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/source_removal.py 41 0 100%
app/rag/sources_meta.py 16 0 100%
app/rag/suggestions.py 27 0 100%
app/rag/summarizer.py 24 0 100%
app/schemas.py 205 0 100%
-----------------------------------------------
TOTAL 2722 12 99%
coverage gate: app/ 99% (>90%) OK
All checks passed!
0 errors, 0 warnings, 0 informations
validation OK
@@ -0,0 +1,14 @@
All task-01 gates green. Final report:
**Task 01 complete — `ls` / `read(path)` / `grep(pattern, path?)` tool surface in `app/rag/agent.py`**
- `AGENT_TOOLS` → exactly `ls` (optional `path`), `read` (required `path`), `grep` (required `pattern`, optional `path`) with the task's pinned descriptions; old names gone from `agent.py` (verified `rg` → no matches)
- `_execute_tool`: `read`/`grep` take the canonical combined `source/path` (first-slash split via new `_resolve_path`; bare source name → no-document refusal, no DB); `ls` scoping by registered source name (`No source named '…'` refusal; `0 documents:` counted); phase-68 A5 grep contract + refusals/round-cap/kill-switch unchanged; split-teaching branches deleted
- New module-level accessor `list_source_names` (registry via `effective_sources` + phase-69 `resolve_source_name`) — the catalog can't distinguish "known source, 0 docs" from "unknown source", the registry can
- Tests: `tests/unit/test_agent.py` rewritten (57 tests, new schema/ls-scope/read/grep pins); `tests/integration/test_agent_tools.py` updated to the new surface incl. real-DB scoped-`ls` registry tests
**Gates:** `pytest tests/unit/test_agent.py --no-cov` → 57 passed · `pytest --cov=app -k agent` → 76 passed, `app/rag/agent.py` **100%** · `ruff check .` clean · `pyright` 0 errors · full suite 1379 passed, **2 failed** — both in `tests/integration/test_chat_api.py` (they script the *old* tool names; fixing them requires `app/api/chat.py`'s SSE `argument` re-derivation, which is task 03's explicit work item — left for it, per no-next-task rule)
**Decisions:** blank/non-string `ls` `path` = omitted (full catalog, not refusal); already-in-context dedupe runs pre-DB (seed docs never hit the DB); no commit (task 05 owns it).
**Next pending task:** `.agents/phases/todo/70_harness_aligned_tools/02_prompt_section.md`
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=================================== FAILURES ===================================
__________ test_grounded_turn_streams_tool_frames_and_cites_read_doc ___________
client = <starlette.testclient.TestClient object at 0x7fc9c0134130>
db = <sqlalchemy.orm.session.Session object at 0x7fc9b02627b0>
seeded_kb = <test_chat_api.FakeRagLLM object at 0x7fc9b0535190>
caplog = <_pytest.logging.LogCaptureFixture object at 0x7fc9b01fcad0>
def test_grounded_turn_streams_tool_frames_and_cites_read_doc(
client, db, seeded_kb: FakeRagLLM, caplog: pytest.LogCaptureFixture
) -> None:
"""(a) Grounded turn with tool calls: the event sequence is
``thinking?/tool/tool/delta…/done``; ``done.sources`` and the
``query_log`` row include the read document (deduped, order
preserved); the per-turn log line carries ``tool_calls=2``.
Phase 45: the agent loop keeps offering the tools for the whole
turn — the round cap (not per-tool budgets) is the bound."""
scripted = FakeRagLLM(
tool_script=[
[
StreamPiece("thinking", "Let me list what is indexed…"),
ToolCallPiece(id="call_1", name="list_documents", arguments={}),
],
[
ToolCallPiece(
id="call_2",
name="read_document",
arguments={"source": "docs", "path": "homelab/backups.md"},
)
],
# the answer request still carries the tools (2 rounds < the
# default cap of 10); the fake's tool_script is exhausted, so
# it falls back to the thinking + answer stream
]
)
fastapi_app.dependency_overrides[chat_api.get_llm] = lambda: scripted
try:
caplog.set_level(logging.INFO, logger="app.chat")
_, _, frames = _stream_chat(client, QUESTION)
finally:
fastapi_app.dependency_overrides.clear()
types = [f["type"] for f in frames]
assert types[0] == "thinking"
assert types[1] == "tool" and types[2] == "tool" # the two executed calls
assert "error" not in types
assert types[3:-1] == ["delta"] * (len(types) - 4) # deltas, then done last
assert frames[-1]["type"] == "done"
list_frame, read_frame = frames[1], frames[2]
assert set(list_frame) == {"type", "name", "argument"}
assert list_frame["name"] == "list_documents"
assert list_frame["argument"] is None # the tool takes no parameters
assert set(read_frame) == {"type", "name", "argument"}
assert read_frame["name"] == "read_document"
assert read_frame["argument"] == "docs/homelab/backups.md"
deltas = [f for f in frames if f["type"] == "delta"]
assert len(deltas) >= 2 # genuinely streamed
assert "".join(d["text"] for d in deltas) == scripted.answer
done = frames[-1]
assert done["deflected"] is False
# done.sources = the retrieval docs + the read doc, deduped, order kept.
sources = [(s["source"], s["path"]) for s in done["sources"]]
> assert sources[-1] == ("docs", "homelab/backups.md") # the read doc is cited
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
E AssertionError: assert ('docs', 'hom...es/deploy.j2') == ('docs', 'homelab/backups.md')
E
E At index 1 diff: 'homelab/templates/deploy.j2' != 'homelab/backups.md'
E Use -v to get more diff
tests/integration/test_chat_api.py:597: AssertionError
---------------------------- Captured stdout setup -----------------------------
2026-09-03 09:53:07 INFO app.importer :: import: added source=docs path=deployments/new-service.md chunks=4
2026-09-03 09:53:07 INFO app.importer :: import: added source=docs path=homelab/backups.md chunks=5
2026-09-03 09:53:07 INFO app.importer :: import: added source=docs path=homelab/container_gitlab/gitlab-compose.yaml chunks=1
2026-09-03 09:53:07 INFO app.importer :: import: summary source=docs path=homelab/container_gitlab/gitlab-compose.yaml chars=70
2026-09-03 09:53:07 INFO app.importer :: import: added source=docs path=homelab/container_gitlab/gitlab.md chunks=4
2026-09-03 09:53:07 INFO app.importer :: import: added source=docs path=homelab/kubernetes.md chunks=5
2026-09-03 09:53:07 INFO app.importer :: import: added source=docs path=homelab/networking/static-dns.json chunks=1
2026-09-03 09:53:07 INFO app.importer :: import: summary source=docs path=homelab/networking/static-dns.json chars=60
2026-09-03 09:53:07 INFO app.importer :: import: added source=docs path=homelab/quadlet/cache.volume chunks=1
2026-09-03 09:53:07 INFO app.importer :: import: summary source=docs path=homelab/quadlet/cache.volume chars=54
2026-09-03 09:53:07 INFO app.importer :: import: added source=docs path=homelab/quadlet/compose.container chunks=2
2026-09-03 09:53:07 INFO app.importer :: import: summary source=docs path=homelab/quadlet/compose.container chars=59
2026-09-03 09:53:07 INFO app.importer :: import: added source=docs path=homelab/quadlet/lan.network chunks=1
2026-09-03 09:53:07 INFO app.importer :: import: summary source=docs path=homelab/quadlet/lan.network chars=53
2026-09-03 09:53:07 INFO app.importer :: import: added source=docs path=homelab/scripts/uptime_probe.py chunks=2
2026-09-03 09:53:07 INFO app.importer :: import: summary source=docs path=homelab/scripts/uptime_probe.py chars=65
2026-09-03 09:53:07 INFO app.importer :: import: added source=docs path=homelab/ssh/ssh_aliases.txt chunks=1
2026-09-03 09:53:07 INFO app.importer :: import: summary source=docs path=homelab/ssh/ssh_aliases.txt chars=55
2026-09-03 09:53:07 INFO app.importer :: import: added source=docs path=homelab/tables.md chunks=2
2026-09-03 09:53:07 INFO app.importer :: import: added source=docs path=homelab/templates/deploy.j2 chunks=1
2026-09-03 09:53:07 INFO app.importer :: import: summary source=docs path=homelab/templates/deploy.j2 chars=54
2026-09-03 09:53:07 INFO app.importer :: import: summary files=13 added=13 updated=0 unchanged=0 pruned=0 errors=0 chunks=30 embed_batches=21 summaries=8 summary_errors=0 formats=md:5,container:1,j2:1,json:1,network:1,py:1,txt:1,volume:1,yaml:1
------------------------------ Captured log setup ------------------------------
INFO app.importer:importer.py:322 import: added source=docs path=deployments/new-service.md chunks=4
INFO app.importer:importer.py:322 import: added source=docs path=homelab/backups.md chunks=5
INFO app.importer:importer.py:322 import: added source=docs path=homelab/container_gitlab/gitlab-compose.yaml chunks=1
INFO app.importer:importer.py:377 import: summary source=docs path=homelab/container_gitlab/gitlab-compose.yaml chars=70
INFO app.importer:importer.py:322 import: added source=docs path=homelab/container_gitlab/gitlab.md chunks=4
INFO app.importer:importer.py:322 import: added source=docs path=homelab/kubernetes.md chunks=5
INFO app.importer:importer.py:322 import: added source=docs path=homelab/networking/static-dns.json chunks=1
INFO app.importer:importer.py:377 import: summary source=docs path=homelab/networking/static-dns.json chars=60
INFO app.importer:importer.py:322 import: added source=docs path=homelab/quadlet/cache.volume chunks=1
INFO app.importer:importer.py:377 import: summary source=docs path=homelab/quadlet/cache.volume chars=54
INFO app.importer:importer.py:322 import: added source=docs path=homelab/quadlet/compose.container chunks=2
INFO app.importer:importer.py:377 import: summary source=docs path=homelab/quadlet/compose.container chars=59
INFO app.importer:importer.py:322 import: added source=docs path=homelab/quadlet/lan.network chunks=1
INFO app.importer:importer.py:377 import: summary source=docs path=homelab/quadlet/lan.network chars=53
INFO app.importer:importer.py:322 import: added source=docs path=homelab/scripts/uptime_probe.py chunks=2
INFO app.importer:importer.py:377 import: summary source=docs path=homelab/scripts/uptime_probe.py chars=65
INFO app.importer:importer.py:322 import: added source=docs path=homelab/ssh/ssh_aliases.txt chunks=1
INFO app.importer:importer.py:377 import: summary source=docs path=homelab/ssh/ssh_aliases.txt chars=55
INFO app.importer:importer.py:322 import: added source=docs path=homelab/tables.md chunks=2
INFO app.importer:importer.py:322 import: added source=docs path=homelab/templates/deploy.j2 chunks=1
INFO app.importer:importer.py:377 import: summary source=docs path=homelab/templates/deploy.j2 chars=54
INFO app.importer:importer.py:103 import: summary files=13 added=13 updated=0 unchanged=0 pruned=0 errors=0 chunks=30 embed_batches=21 summaries=8 summary_errors=0 formats=md:5,container:1,j2:1,json:1,network:1,py:1,txt:1,volume:1,yaml:1
----------------------------- Captured stdout call -----------------------------
2026-09-03 09:53:07 INFO app.agent :: agent tool=list_documents args={} round=1/10
2026-09-03 09:53:07 INFO app.agent :: agent tool=read_document args={"source": "docs", "path": "homelab/backups.md"} round=2/10
2026-09-03 09:53:07 INFO app.chat :: question='How is my Kubernetes cluster set up?' embed_ms=0 top_score=0.436 fts_hits=4 summary_hits=1 tuning=0 kb_chars=0 threshold=0.30 deflected=False sources=['docs/homelab/kubernetes.md', 'docs/homelab/templates/deploy.j2'] thinking_chars=28 tool_calls=0 total_ms=11 retries=0
------------------------------ Captured log call -------------------------------
INFO app.agent:agent.py:527 agent tool=list_documents args={} round=1/10
INFO app.agent:agent.py:527 agent tool=read_document args={"source": "docs", "path": "homelab/backups.md"} round=2/10
INFO app.chat:chat.py:506 question='How is my Kubernetes cluster set up?' embed_ms=0 top_score=0.436 fts_hits=4 summary_hits=1 tuning=0 kb_chars=0 threshold=0.30 deflected=False sources=['docs/homelab/kubernetes.md', 'docs/homelab/templates/deploy.j2'] thinking_chars=28 tool_calls=0 total_ms=11 retries=0
______________ test_tool_execution_db_failure_yields_error_event _______________
client = <starlette.testclient.TestClient object at 0x7fc9b0eea0b0>
db = <sqlalchemy.orm.session.Session object at 0x7fc9b02d27b0>
seeded_kb = <test_chat_api.FakeRagLLM object at 0x7fc9b0535610>
monkeypatch = <_pytest.monkeypatch.MonkeyPatch object at 0x7fc9c35c3d20>
def test_tool_execution_db_failure_yields_error_event(
client, db, seeded_kb: FakeRagLLM, monkeypatch: pytest.MonkeyPatch
) -> None:
"""A tool call that hits a dead DB mid-stream gets the same structured
``error`` event as the pre-stream retrieval path — never a severed
stream (the "never stale" contract, PLAN §7.4)."""
scripted = FakeRagLLM(
tool_script=[[ToolCallPiece(id="call_1", name="list_documents", arguments={})]]
)
def boom(*_a: Any, **_k: Any) -> Any:
raise RuntimeError("db exploded mid tool call")
monkeypatch.setattr(agent, "list_catalog", boom)
fastapi_app.dependency_overrides[chat_api.get_llm] = lambda: scripted
try:
_, _, frames = _stream_chat(client, QUESTION)
finally:
fastapi_app.dependency_overrides.clear()
# The ``tool`` frame went out first (the model requested the call);
# the failed execution ends the turn with the structured error event.
> assert [f["type"] for f in frames] == ["tool", "error"]
E AssertionError: assert ['tool', 'del... 'delta', ...] == ['tool', 'error']
E
E At index 1 diff: 'delta' != 'error'
E Left contains 5 more items, first extra item: 'delta'
E Use -v to get more diff
tests/integration/test_chat_api.py:817: AssertionError
---------------------------- Captured stdout setup -----------------------------
2026-09-03 09:53:08 INFO app.importer :: import: added source=docs path=deployments/new-service.md chunks=4
2026-09-03 09:53:08 INFO app.importer :: import: added source=docs path=homelab/backups.md chunks=5
2026-09-03 09:53:08 INFO app.importer :: import: added source=docs path=homelab/container_gitlab/gitlab-compose.yaml chunks=1
2026-09-03 09:53:08 INFO app.importer :: import: summary source=docs path=homelab/container_gitlab/gitlab-compose.yaml chars=70
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2026-09-03 09:53:08 INFO app.importer :: import: added source=docs path=homelab/kubernetes.md chunks=5
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2026-09-03 09:53:08 INFO app.importer :: import: added source=docs path=homelab/quadlet/lan.network chunks=1
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2026-09-03 09:53:08 INFO app.importer :: import: summary source=docs path=homelab/scripts/uptime_probe.py chars=65
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2026-09-03 09:53:08 INFO app.importer :: import: added source=docs path=homelab/templates/deploy.j2 chunks=1
2026-09-03 09:53:08 INFO app.importer :: import: summary source=docs path=homelab/templates/deploy.j2 chars=54
2026-09-03 09:53:08 INFO app.importer :: import: summary files=13 added=13 updated=0 unchanged=0 pruned=0 errors=0 chunks=30 embed_batches=21 summaries=8 summary_errors=0 formats=md:5,container:1,j2:1,json:1,network:1,py:1,txt:1,volume:1,yaml:1
------------------------------ Captured log setup ------------------------------
INFO app.importer:importer.py:322 import: added source=docs path=deployments/new-service.md chunks=4
INFO app.importer:importer.py:322 import: added source=docs path=homelab/backups.md chunks=5
INFO app.importer:importer.py:322 import: added source=docs path=homelab/container_gitlab/gitlab-compose.yaml chunks=1
INFO app.importer:importer.py:377 import: summary source=docs path=homelab/container_gitlab/gitlab-compose.yaml chars=70
INFO app.importer:importer.py:322 import: added source=docs path=homelab/container_gitlab/gitlab.md chunks=4
INFO app.importer:importer.py:322 import: added source=docs path=homelab/kubernetes.md chunks=5
INFO app.importer:importer.py:322 import: added source=docs path=homelab/networking/static-dns.json chunks=1
INFO app.importer:importer.py:377 import: summary source=docs path=homelab/networking/static-dns.json chars=60
INFO app.importer:importer.py:322 import: added source=docs path=homelab/quadlet/cache.volume chunks=1
INFO app.importer:importer.py:377 import: summary source=docs path=homelab/quadlet/cache.volume chars=54
INFO app.importer:importer.py:322 import: added source=docs path=homelab/quadlet/compose.container chunks=2
INFO app.importer:importer.py:377 import: summary source=docs path=homelab/quadlet/compose.container chars=59
INFO app.importer:importer.py:322 import: added source=docs path=homelab/quadlet/lan.network chunks=1
INFO app.importer:importer.py:377 import: summary source=docs path=homelab/quadlet/lan.network chars=53
INFO app.importer:importer.py:322 import: added source=docs path=homelab/scripts/uptime_probe.py chunks=2
INFO app.importer:importer.py:377 import: summary source=docs path=homelab/scripts/uptime_probe.py chars=65
INFO app.importer:importer.py:322 import: added source=docs path=homelab/ssh/ssh_aliases.txt chunks=1
INFO app.importer:importer.py:377 import: summary source=docs path=homelab/ssh/ssh_aliases.txt chars=55
INFO app.importer:importer.py:322 import: added source=docs path=homelab/tables.md chunks=2
INFO app.importer:importer.py:322 import: added source=docs path=homelab/templates/deploy.j2 chunks=1
INFO app.importer:importer.py:377 import: summary source=docs path=homelab/templates/deploy.j2 chars=54
INFO app.importer:importer.py:103 import: summary files=13 added=13 updated=0 unchanged=0 pruned=0 errors=0 chunks=30 embed_batches=21 summaries=8 summary_errors=0 formats=md:5,container:1,j2:1,json:1,network:1,py:1,txt:1,volume:1,yaml:1
----------------------------- Captured stdout call -----------------------------
2026-09-03 09:53:08 INFO app.agent :: agent tool=list_documents args={} round=1/10
2026-09-03 09:53:08 INFO app.chat :: question='How is my Kubernetes cluster set up?' embed_ms=0 top_score=0.436 fts_hits=4 summary_hits=1 tuning=0 kb_chars=0 threshold=0.30 deflected=False sources=['docs/homelab/kubernetes.md', 'docs/homelab/templates/deploy.j2'] thinking_chars=0 tool_calls=0 total_ms=10 retries=0
------------------------------ Captured log call -------------------------------
INFO app.agent:agent.py:527 agent tool=list_documents args={} round=1/10
INFO app.chat:chat.py:506 question='How is my Kubernetes cluster set up?' embed_ms=0 top_score=0.436 fts_hits=4 summary_hits=1 tuning=0 kb_chars=0 threshold=0.30 deflected=False sources=['docs/homelab/kubernetes.md', 'docs/homelab/templates/deploy.j2'] thinking_chars=0 tool_calls=0 total_ms=10 retries=0
=============================== 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 153 4 97%
app/api/chats.py 110 0 100%
app/api/config.py 7 0 100%
app/api/doc_drafts.py 93 0 100%
app/api/docs.py 50 0 100%
app/api/git_sources.py 212 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 101 0 100%
app/config.py 126 0 100%
app/core/__init__.py 0 0 100%
app/core/auth.py 20 0 100%
app/core/caching.py 108 0 100%
app/core/debugging.py 29 2 93%
app/core/docs_push.py 39 0 100%
app/core/logging.py 13 0 100%
app/db.py 21 0 100%
app/main.py 52 0 100%
app/models.py 86 0 100%
app/rag/__init__.py 0 0 100%
app/rag/agent.py 139 0 100%
app/rag/archive_upload.py 128 0 100%
app/rag/chunker.py 206 4 98%
app/rag/git_sources.py 14 0 100%
app/rag/importer.py 180 3 98%
app/rag/llm.py 213 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/source_removal.py 41 0 100%
app/rag/sources_meta.py 16 0 100%
app/rag/suggestions.py 27 0 100%
app/rag/summarizer.py 24 0 100%
app/schemas.py 205 0 100%
-----------------------------------------------
TOTAL 2726 16 99%
=========================== short test summary info ============================
FAILED tests/integration/test_chat_api.py::test_grounded_turn_streams_tool_frames_and_cites_read_doc
FAILED tests/integration/test_chat_api.py::test_tool_execution_db_failure_yields_error_event
tests FAILED: unit + integration suite did not pass
All checks passed!
0 errors, 0 warnings, 0 informations
validation FAILED (see output above)
@@ -0,0 +1,11 @@
All gates green — full suite included. Final report:
**Fixed:** the harness gate runs the full unit+integration suite, so I resolved the two `test_chat_api.py` failures that the phase plans queue for task 03 — the minimal coupled fix, no further task-03 work:
- `app/api/chat.py`: SSE `tool`-frame `argument` re-derived for the new surface — `read`'s `path` (combined `source/path`), `grep`'s `pattern`, `ls`'s `path`, else/null for non-strings or unknown tools; module docstring + inline comments updated (old names now gone from `chat.py` too)
- `tests/integration/test_chat_api.py`: 5 tests moved to the new surface — `ls`+`read(path=…)` frame test (`argument` == the single string the model passed), search-frame test renamed to `grep` (raw pattern / non-string → null), DB-failure test scripted as `ls` (asserts `name == "ls"`, `["tool","error"]`), deflected + kill-switch scripts renamed
**Results:** `uv run pytest` → **1381 passed, 0 failed** · `--cov=app` TOTAL **99%** (`app/rag/agent.py` 100%, `app/api/chat.py` 100%) · `uv run pytest tests/unit/test_agent.py --no-cov` → 57 passed · `uv run pytest --cov=app -k agent` → 76 passed · `uv run ruff check .` clean · `uv run pyright` 0 errors · `rg` old names in `app/rag/agent.py` → no matches
**Decisions:** remaining old-name test references (chats_api, sse_events, mock_tool_flow, frontend_tool_states, llm_*) all pass — they pin opaque data or files owned by tasks 02/04/05, left untouched; deflected path + kill switch byte-identical (pinned).
**Next pending task:** `.agents/phases/todo/70_harness_aligned_tools/02_prompt_section.md`
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=============================== 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 149 0 100%
app/api/chats.py 110 0 100%
app/api/config.py 7 0 100%
app/api/doc_drafts.py 93 0 100%
app/api/docs.py 50 0 100%
app/api/git_sources.py 212 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 101 0 100%
app/config.py 126 0 100%
app/core/__init__.py 0 0 100%
app/core/auth.py 20 0 100%
app/core/caching.py 108 0 100%
app/core/debugging.py 29 2 93%
app/core/docs_push.py 39 0 100%
app/core/logging.py 13 0 100%
app/db.py 21 0 100%
app/main.py 52 0 100%
app/models.py 86 0 100%
app/rag/__init__.py 0 0 100%
app/rag/agent.py 139 0 100%
app/rag/archive_upload.py 128 0 100%
app/rag/chunker.py 206 4 98%
app/rag/git_sources.py 14 0 100%
app/rag/importer.py 180 3 98%
app/rag/llm.py 213 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/source_removal.py 41 0 100%
app/rag/sources_meta.py 16 0 100%
app/rag/suggestions.py 27 0 100%
app/rag/summarizer.py 24 0 100%
app/schemas.py 205 0 100%
-----------------------------------------------
TOTAL 2722 12 99%
coverage gate: app/ 99% (>90%) OK
All checks passed!
0 errors, 0 warnings, 0 informations
validation OK
@@ -0,0 +1,19 @@
Task 02 complete — all gates green.
**Implemented**
- `app/rag/prompts.py`: rewrote `TOOLS_SECTION` copy for the harness-aligned `ls` / `read(path)` / `grep(pattern, path?)` shapes (catalog-line format, case-insensitive locator contract, combined `source/path` + full content, answer-when-ready close — no budget re-statement, phase 45); updated the module docstring and section comment (HIGH-only, LOW byte-identical, mock keys on `<tools>` marker presence); `build_high_prompt`/`build_deflect_prompt` and section order untouched
- `tests/unit/test_prompts.py`: new phase-70 pin block (markers, shape copy pins, old names + budget copy absent, HIGH still ends with `<tools>`), explicit no-`<tools>`/no-new-copy LOW assertions
- `tests/unit/test_chat_gate.py`: endpoint pins updated (new names in HIGH system prompt, old names out; new copy absent from the deflected path)
- `tests/unit/test_agent.py`: re-pinned the old `TOOLS_SECTION` copy pins (the in-file NOTE delegated this re-pin to task 02)
**Results**
- `uv run pytest tests/unit/test_prompts.py tests/unit/test_chat_gate.py -v --no-cov` → 58 passed
- `rg "list_documents|read_document|search_documents" app/rag/prompts.py` → no matches
- `uv run pytest --cov=app --cov-report=term-missing` → 1385 passed; `app/rag/prompts.py` 100% (>90% gate), TOTAL 99%
- `uv run ruff check . && uv run pyright` → All checks passed / 0 errors
**Decisions**
- E2E/mock still on old names — expected mid-phase; task 05 owns the mock + E2E updates (default `testpaths` excludes E2E; mock keys on the `<tools>` marker only, so keying is intact)
- No PLAN.md exists in `.agents/` (referenced by AGENTS.md); the phase overview was treated as binding context
**Next pending task:** `.agents/phases/todo/70_harness_aligned_tools/03_api_sse.md`
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=============================== 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 149 0 100%
app/api/chats.py 110 0 100%
app/api/config.py 7 0 100%
app/api/doc_drafts.py 93 0 100%
app/api/docs.py 50 0 100%
app/api/git_sources.py 212 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 101 0 100%
app/config.py 126 0 100%
app/core/__init__.py 0 0 100%
app/core/auth.py 20 0 100%
app/core/caching.py 108 0 100%
app/core/debugging.py 29 2 93%
app/core/docs_push.py 39 0 100%
app/core/logging.py 13 0 100%
app/db.py 21 0 100%
app/main.py 52 0 100%
app/models.py 86 0 100%
app/rag/__init__.py 0 0 100%
app/rag/agent.py 139 0 100%
app/rag/archive_upload.py 128 0 100%
app/rag/chunker.py 206 4 98%
app/rag/git_sources.py 14 0 100%
app/rag/importer.py 180 3 98%
app/rag/llm.py 213 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/source_removal.py 41 0 100%
app/rag/sources_meta.py 16 0 100%
app/rag/suggestions.py 27 0 100%
app/rag/summarizer.py 24 0 100%
app/schemas.py 205 0 100%
-----------------------------------------------
TOTAL 2722 12 99%
coverage gate: app/ 99% (>90%) OK
All checks passed!
0 errors, 0 warnings, 0 informations
validation OK
@@ -0,0 +1,16 @@
All gates green. Task 03 is complete.
**Task 03 — SSE `tool` frames + API contract copy: done**
- `app/api/chat.py`: `ToolCallPiece` → SSE derivation now symmetric — `argument` = the single string the model passed (`read`/`ls` → `path`, `grep` → `pattern`), non-string/omitted → null; module docstring carries the phase-70 note, the `{"type":"tool",…}` shape, and the `done.sources`/`query_log`/`tool_calls=N` contract (verified in place; branch was already rewritten by the earlier interrupted run of this task).
- `app/schemas.py`: `ChatToolEvent` docstring re-pointed at `ls`/`read`/`grep` + the argument rule (no field change); `ToolCall` docstring updated incl. the locked no-migration note for legacy saved names.
- `tests/integration/test_chat_api.py`: new pin `test_tool_frames_carry_the_model_arguments_regardless_of_execution` — scoped `ls` frame carries `"docs"`; a rejected `read` (unknown path) still emits its frame with the model's argument as passed; `done.sources` stays retrieval-only; log line `tool_calls=1` (rejected calls count nothing). Existing pins: `read` frame = combined path as passed, `grep` frame = pattern, unscoped `ls` = null.
- `tests/integration/test_chats_api.py`: saved-chat fixture on new names/args; keeps one `read_document` entry pinning that pre-phase-70 chats still validate (locked, no migration).
**Results**
- `uv run pytest tests/integration/test_agent_tools.py tests/integration/test_chat_api.py -v --no-cov` → 40 passed
- `uv run pytest tests/integration/test_chats_api.py --no-cov` → 54 passed; full `uv run pytest` → green (exit 0)
- `uv run pytest --cov=app --cov-report=term-missing` → `app/api/chat.py` 100%, `app/schemas.py` 100%, TOTAL 99% (>90%)
- `uv run ruff check . && uv run pyright` → clean (0 errors)
**Notes**: `tests/integration/test_api.py` old-name mentions are app.js asset pins — left for task 04 (frontend). Legacy docstring names in `app/rag/llm.py` and the `docs.py` route function name fall to the phase-level `rg` gate in task 05. Next pending task: `04_frontend.md`.
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=============================== 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 149 0 100%
app/api/chats.py 110 0 100%
app/api/config.py 7 0 100%
app/api/doc_drafts.py 93 0 100%
app/api/docs.py 50 0 100%
app/api/git_sources.py 212 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 101 0 100%
app/config.py 126 0 100%
app/core/__init__.py 0 0 100%
app/core/auth.py 20 0 100%
app/core/caching.py 108 0 100%
app/core/debugging.py 29 2 93%
app/core/docs_push.py 39 0 100%
app/core/logging.py 13 0 100%
app/db.py 21 0 100%
app/main.py 52 0 100%
app/models.py 86 0 100%
app/rag/__init__.py 0 0 100%
app/rag/agent.py 139 0 100%
app/rag/archive_upload.py 128 0 100%
app/rag/chunker.py 206 4 98%
app/rag/git_sources.py 14 0 100%
app/rag/importer.py 180 3 98%
app/rag/llm.py 213 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/source_removal.py 41 0 100%
app/rag/sources_meta.py 16 0 100%
app/rag/suggestions.py 27 0 100%
app/rag/summarizer.py 24 0 100%
app/schemas.py 205 0 100%
-----------------------------------------------
TOTAL 2722 12 99%
coverage gate: app/ 99% (>90%) OK
All checks passed!
0 errors, 0 warnings, 0 informations
validation OK
@@ -0,0 +1,11 @@
All green. The other modified files are uncommitted work from completed tasks 01–03 (the commit belongs to task 05 per the phase plan).
**Task 04 report**
- `frontend/assets/app.js`: `appendToolLine` now keys on `read`/`grep`/`ls` (new copy: "📄 Reading", "🔎 Searching for", "🔎 Listing documents in <scope>", unscoped "🔎 Listing documents") with legacy `read_document`/`search_documents`/`list_documents` branches preserved byte-identical for persisted turns; status-label ternary in the turn handler extended to the new names (incl. scoped `ls`); section + module docstrings updated with the phase-70 note.
- `frontend/assets/shared.js`: `addToolLines` local copy got the same new-name branches (read/grep/ls + scoped ls) with the legacy branches kept; all arguments `textContent`-only; docstring updated.
- `tests/unit/test_frontend_tool_states.py`: pins updated/added — new+legacy branch gates in app.js, new shared.js pin test (`test_shared_page_tool_lines_cover_new_and_legacy_names`), no-`innerHTML` textContent discipline; old copy pins kept.
- Ripple fix: `tests/integration/test_api.py` emoji guard now strips the fourth tool-line literal `"🔎 Listing documents in "`.
- Tests: `uv run pytest tests/unit/test_frontend_tool_states.py -v --no-cov` → 10 passed; `uv run pytest --cov=app --cov-report=term-missing` → 1387 passed, TOTAL 99% (>90%); `uv run ruff check . && uv run pyright` → clean; both JS files pass `node --check`.
- Decisions: explicit if-chains (not a name map) for the two-generation gates; scoped-`ls` status label added so the live region mirrors the new line copy (PLAN §7.4). E2E suites remain keyed on the old mock names — task 05's scope.
- Next pending task: `.agents/phases/todo/70_harness_aligned_tools/05_mock_e2e_commit.md`.
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=============================== 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 149 0 100%
app/api/chats.py 110 0 100%
app/api/config.py 7 0 100%
app/api/doc_drafts.py 93 0 100%
app/api/docs.py 50 0 100%
app/api/git_sources.py 212 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 101 0 100%
app/config.py 126 0 100%
app/core/__init__.py 0 0 100%
app/core/auth.py 20 0 100%
app/core/caching.py 108 0 100%
app/core/debugging.py 29 2 93%
app/core/docs_push.py 39 0 100%
app/core/logging.py 13 0 100%
app/db.py 21 0 100%
app/main.py 52 0 100%
app/models.py 86 0 100%
app/rag/__init__.py 0 0 100%
app/rag/agent.py 139 0 100%
app/rag/archive_upload.py 128 0 100%
app/rag/chunker.py 206 4 98%
app/rag/git_sources.py 14 0 100%
app/rag/importer.py 180 3 98%
app/rag/llm.py 213 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/source_removal.py 41 0 100%
app/rag/sources_meta.py 16 0 100%
app/rag/suggestions.py 27 0 100%
app/rag/summarizer.py 24 0 100%
app/schemas.py 205 0 100%
-----------------------------------------------
TOTAL 2722 12 99%
coverage gate: app/ 99% (>90%) OK
All checks passed!
0 errors, 0 warnings, 0 informations
validation OK
@@ -0,0 +1,20 @@
Done — the empty `.err` is a harness runtime artifact (tracked-report convention, same as prior phases); working tree is clean.
**Phase 70, task 05 complete**
- `tests/e2e/mock_llm.py`: deterministic flows now emit `ls` (no args, `call_0`), `read` with the **combined** `source/path` (mock joins the two catalog fields — only parse change), `grep` with `pattern`; docstrings + phase-70 notes updated
- Existing E2E suites updated to new frames: `test_agent_document_tools.py` (`ls`→`read`), `test_agent_unlimited_tools.py` (multi-read `ls`+2×`read`), `test_search_tool.py` (`grep` + pattern argument)
- NEW `tests/e2e/test_harness_aligned_tools.py` (3 tests): READ flow (ls line → 📄 Reading line → quoted answer → done.sources incl. read doc → no raw `<|…|>`/`tool_call` markup in DOM), SEARCH flow (🔎 Searching for sentinel → answer), wire argument rule across both flows (ls→null, read→combined path, grep→pattern; names ⊆ {ls, read, grep})
- README agent-tools section rewritten for `ls`/`read(path)`/`grep(pattern, path?)` (combined identity + A5 locator semantics); `.env.example` header comment refreshed
- Old-name cleanup so the rg criterion holds: `app/api/docs.py` route fn → `list_indexed_documents`, `app/rag/llm.py` docstrings, `test_llm_client.py`, `test_llm_stream_teardown.py`, `test_sse_events.py`, `test_mock_tool_flow.py`, `test_api.py` docstring. Remaining matches: only the explicitly-marked legacy frontend branches/pins + the marked legacy-chat persistence pin + the mandated "old names absent" regression pins from tasks 01–02
**Gates (all green):**
- `uv run pytest` → exit 0; `uv run pytest --cov=app --cov-report=term-missing` → TOTAL **99%** (>90%)
- `uv run ruff check .` → clean; `uv run pyright` → 0 errors
- E2E in isolation: `test_harness_aligned_tools` 3 passed, `test_agent_document_tools` 4, `test_agent_unlimited_tools` 4, `test_search_tool` 3, `test_chat_rag` 3
**Decisions:** mock `_tool_flow` tuple kept `(source, path)`; the join happens at the wire-emission point (keeps `test_mock_tool_flow.py` pins valid). `.env.example` included in the commit for atomicity (not in the block's path list, but task 05 touched it). Phase-dir move left to the harness per executor rules.
**Commit:** `801639e feat(agent): align the document tools with the harness-trained shape — ls, read(path), grep(pattern, path?)` (55 files, `--no-gpg-sign`)
**Next pending:** `71_scaffolding_guardrails/01_filter.md`
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=============================== 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 149 0 100%
app/api/chats.py 110 0 100%
app/api/config.py 7 0 100%
app/api/doc_drafts.py 93 0 100%
app/api/docs.py 50 0 100%
app/api/git_sources.py 212 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 101 0 100%
app/config.py 126 0 100%
app/core/__init__.py 0 0 100%
app/core/auth.py 20 0 100%
app/core/caching.py 108 0 100%
app/core/debugging.py 29 2 93%
app/core/docs_push.py 39 0 100%
app/core/logging.py 13 0 100%
app/db.py 21 0 100%
app/main.py 52 0 100%
app/models.py 86 0 100%
app/rag/__init__.py 0 0 100%
app/rag/agent.py 139 0 100%
app/rag/archive_upload.py 128 0 100%
app/rag/chunker.py 206 4 98%
app/rag/git_sources.py 14 0 100%
app/rag/importer.py 180 3 98%
app/rag/llm.py 213 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/source_removal.py 41 0 100%
app/rag/sources_meta.py 16 0 100%
app/rag/suggestions.py 27 0 100%
app/rag/summarizer.py 24 0 100%
app/schemas.py 205 0 100%
-----------------------------------------------
TOTAL 2722 12 99%
coverage gate: app/ 99% (>90%) OK
All checks passed!
0 errors, 0 warnings, 0 informations
validation OK