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/45_agent_unlimited_tools/00_phase.md

@@ -0,0 +1,42 @@
+# Phase 45 — Agent makes as many tool calls as it wants
+
+**Source:** `TODO.md` L8 — "Allow the LLM to make as many tool calls as it wants, remove the restrictions, they're causing problems getting correct answers"
+**Story:** `.agents/user_stories/agent-unlimited-tools.md`
+**Context:** Phase 37 shipped the grounded-turn agent loop (`app/rag/agent.py::run_agent`) with per-turn budgets — `agent_list_calls` / `agent_read_calls` (default 1 each, `BOR_AGENT_LIST_CALLS` / `BOR_AGENT_READ_CALLS`), "budgets-as-kill-switch" locked decision. The exhaustion refusals (`LIST_EXHAUSTED` / `READ_EXHAUSTED`) are where correct multi-document answers die. Owner direction (2026-08-27): remove both budgets; the loop keeps one guard — a configurable **round cap** that also doubles as the no-tools kill switch (`0`).
+
+## Objective
+`list_documents` / `read_document` can be called as many times as the model needs (re-lists included), bounded only by `BOR_AGENT_MAX_ROUNDS` (default 10; `0` = no tools, byte-identical to the pre-phase-37 path).
+
+## Dependencies
+- `44_markdown_tables` (todo) — sequential only (no shared files: this phase is `app/` + tests + mock).
+- `37_agent_document_tools` (complete) — the loop, the `tool` SSE event, the UI tool lines, the per-turn `tool_calls=N` log field, and the phase-37 locked decision being revised.
+- `31_kb_overview_prompt` (complete) — the `lite` one-shot path is untouched by this phase.
+
+## Tasks
+1. `01_config_round_cap.md` — the server core, atomically: `agent_max_rounds` replaces the budgets in `app/config.py` + `app/rag/agent.py`, unit + integration rewrites, `.env.example` (one task so the per-task gate stays green).
+2. `02_mock_multi_read_flow.md` — the E2E mock's deterministic multi-read (list → read #1 → read #2 → answer) flow.
+3. `03_unlimited_tools_e2e_and_commit.md` — story E2E + phase-37 regression + PLAN.md revision note + commit.
+
+## Testing & Quality
+- Unit: `tests/unit/test_agent.py` rewritten around the round cap (always-calling mock LLM: N tool rounds then a forced `tools=None` final answer; `max_rounds=0` → exactly one request with `tools=None`; rejected-call spam — unknown tool / already-in-context — is bounded by the cap, not by budgets; re-lists execute and count in `tool_calls`); `tests/unit/test_config.py` (default 10, `BOR_AGENT_MAX_ROUNDS` override, `0`, the budget env vars are gone).
+- Integration: `tests/integration/test_chat_api.py` — the `agent_list_calls=0, agent_read_calls=0` fixtures become `agent_max_rounds=0`; the tool SSE event shape and the `done.sources` extension assertions stay.
+- Coverage: **>90%** on `app/` — `agent.py` + `config.py` fully covered.
+- E2E (mandatory, A16): `tests/e2e/test_agent_unlimited_tools.py`, run in isolation.
+
+## Completion Criteria
+- [ ] `BOR_AGENT_LIST_CALLS` / `BOR_AGENT_READ_CALLS` are gone (config, `.env.example`, agent, tests); no exhaustion refusal remains.
+- [ ] A multi-read turn (list + 2 reads) streams three tool lines, answers non-deflected, and `done.sources` lists the retrieved doc(s) + both reads deduped.
+- [ ] `agent_max_rounds=0` → single `tools=None` request (kill switch); at the cap the loop forces a final no-tools answer (log warning kept).
+- [ ] `tool` SSE event shape and `tool_calls=N` per-turn log field unchanged.
+- [ ] `.agents/PLAN.md` carries the phase-37 revision note (owner permission 2026-08-27, `TODO.md` L8) — the only PLAN edit in this phase.
+- [ ] `uv run pytest` green; `uv run pytest --cov=app --cov-report=term-missing` >90%.
+- [ ] `uv run pytest tests/e2e/test_agent_unlimited_tools.py -v --no-cov` green in isolation (DB up).
+- [ ] Regression E2E suites green in isolation: `test_agent_document_tools.py`, `test_chat_rag.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-locked revision (2026-08-27, roadmap R2):** the phase-37 "budgets-as-kill-switch" decision is **revised** — both per-tool budgets removed; `BOR_AGENT_MAX_ROUNDS` (default 10) is the only loop guard and the kill switch (`0`). Recorded as a PLAN.md revision note (the established owner-permission pattern, like the A10/A7/A9/A15 notes) — a recorded revision, not a silent deviation (AGENTS.md rule 3).
+- **A15 extension unchanged** — the `tool` SSE event shape, the `done` shape, and the per-turn log line (`tool_calls=N`) are untouched; the revision note amends the phase-37 note's budget wording only.
+- **Rejections kept:** `Unknown tool.`, `MISSING_READ_ARGS`, `Already in your context.` (non-budget rejections; the cap bounds their pathological repetition).
+- **A17 honoured** — one atomic commit.

.agents/phases/complete/45_agent_unlimited_tools/03_unlimited_tools_e2e_and_commit.md

@@ -0,0 +1,39 @@
+# Task 03 — Unlimited-tools E2E + PLAN revision note + commit
+
+**Phase:** `45_agent_unlimited_tools` · **Source:** `TODO.md:8` — "Allow the LLM to make as many tool calls as it wants, remove the restrictions, they're causing problems getting correct answers"
+**Story:** `.agents/user_stories/agent-unlimited-tools.md`
+
+## Objective
+Prove the multi-tool turn end to end, record the phase-37 decision revision in PLAN.md, run the regressions, and commit the phase.
+
+## Work
+1. `tests/e2e/test_agent_unlimited_tools.py` (new) — mock-only, DB up (the grounded-turn prerequisite: the fixture KB imported, per the `test_agent_document_tools.py` fixture pattern):
+   - `test_multi_read_turn` — a grounded question carrying `TOOLS_TRIGGER` + `MULTI_READ_TRIGGER`: the turn streams **three** tool lines (`.tool-call` rows: one `list_documents` — "is listing documents" — and two `read_document` — "is reading <source/path>") in order, then a final non-deflected answer containing the mock's "I read <path1> and <path2>." line;
+   - `test_done_sources_include_reads` — the source chips under the answer list the retrieval doc(s) **plus both** read documents, deduped (the phase-37 `done.sources` extension contract, now with 2 reads);
+   - `test_relist_allowed` — the listing tool ran without a "No listing budget left" refusal: assert no refusal text anywhere in the bubble/tool lines (the old refusal strings must be gone — grep the app for them is task 01's job; here assert the UI never shows one);
+   - `test_single_tool_flow_regression` (phase 37) — the original 3-step flow (marker without the multi-read trigger) still answers after exactly one read with its single tool pair (this may be a targeted re-assertion; the full suite `test_agent_document_tools.py` runs in the regression pass).
+2. `.agents/PLAN.md` — **the only PLAN edit in this phase** (owner-locked revision, roadmap R2): in the §4 SSE-revision block, after the phase-37 revision note, add a new note in the established style:
+   > **SSE revision (phase 45, owner permission 2026-08-27):** the phase-37
+   > per-turn tool budgets are **removed** (owner: "allow the LLM to make
+   > as many tool calls as it wants — `TODO.md` L8): `BOR_AGENT_LIST_CALLS`
+   > / `BOR_AGENT_READ_CALLS` no longer exist; `BOR_AGENT_MAX_ROUNDS`
+   > (default 10) caps the tool rounds and `0` disables the tools
+   > entirely (the pre-phase-37 path). The `tool` event shape and the
+   > `done` shape are unchanged — a recorded revision of the phase-37
+   > note's budget wording, not a silent deviation.
+   Also update the phase-37 note's budget clause if it reads as current
+   truth ("budgeted by `BOR_AGENT_LIST_CALLS` / `BOR_AGENT_READ_CALLS`")
+   by appending "(removed in phase 45 — see the revision note below)".
+   Touch **nothing else** in PLAN.md (Protocol B: no roadmap-table edit for appended phases).
+3. Regression pass (isolation runs): `test_agent_document_tools.py` (phase 37 — must pass **unmodified**), `test_chat_rag.py`, `test_smoke.py`.
+4. `uv run pytest` green; `uv run pytest --cov=app --cov-report=term-missing` >90%; `uv run ruff check . && uv run pyright` clean.
+5. Commit (Conventional Commits, `--no-gpg-sign`), e.g. `feat(rag): unbounded agent tool calls behind a round cap (owner revision)`, staging this phase's files **including the force-added `.agents/PLAN.md`** (AGENTS.md rule 8: `git add -f .agents/PLAN.md`) and the phase dir move `.agents/phases/todo/45_agent_unlimited_tools/` → `.agents/phases/complete/`.
+
+## Testing & Quality
+- E2E: `uv run pytest tests/e2e/test_agent_unlimited_tools.py -v --no-cov` green in isolation.
+- Coverage: **>90%** on `app/` (task 01's rewritten tests carry it).
+
+## Completion Criteria
+- [ ] The multi-read E2E suite passes in isolation; the phase-37 suite passes unmodified in isolation.
+- [ ] PLAN.md carries the phase-45 revision note (owner permission 2026-08-27) and nothing else changed.
+- [ ] One atomic `--no-gpg-sign` commit; phase dir moved to `.agents/phases/complete/`.