chore: fix ruff lint findings, restore green CI lint gate

[man4ish]

What

ruff check . (CI's "Lint & Test" job) has been failing on main across the last several merged PRs — 161 pre-existing findings, entirely unrelated to any of the recent security/config/docs work. This restores a green, meaningful lint gate.

Before / after

	Findings
Before	161
After	0 — ruff check . → All checks passed!

Findings by rule code (before)

Code	Count	Category
UP006	52	List/Dict/Set/Tuple → builtin generics
I001	30	import sorting
BLE001	17	blind except Exception
UP035	15	deprecated typing imports
F401	11	unused imports
RUF010	8	unnecessary str() in f-string
RUF013	8	implicit Optional (x: str = None)
SIM117	5	nested with statements
UP045	4	Optional[X] → X | None
F841	4	unused local variable
SIM102	1	collapsible if
UP007	1	Union[X, Y] → X | Y
SIM118	1	key in dict.keys() → key in dict
TRY004	1	wrong exception type for a type check
E722	1	bare except:
S112	1	try/except/continue with no logging
EXE001	1	shebang present but file not executable

What was auto-fixed vs. manually fixed vs. noqa'd

Auto-fixed by ruff check . --fix (safe fixes only) — 121 findings, zero behavior change:
UP006, I001, UP035, F401, RUF010, UP045, UP007 — all pure import reordering / typing modernization (List→list, Optional[X]→X | None, dropping now-unused imports, f"{str(e)}"→f"{e!s}").

Manually fixed (real, minor issues) — 15 findings:

• RUF013 (8, 4 call sites): param: str = None → param: str | None = None in index/vector_store.py and rag/engine.py.
• SIM117 (5): nested with statements in tests collapsed into one parenthesized with (...) — same context managers, purely mechanical.
• SIM102 (1): collapsed a nested if in api/main.py's guard_requests middleware into one condition.
• SIM118 (1): for node in self.edges.keys() → for node in self.edges in index/graph_store.py.
• E722 + S112 (1 site, rag/query_router.py): a bare except: continue around a per-line JSON parse was narrowed to the actual exception types (JSONDecodeError/UnicodeDecodeError/AttributeError/KeyError) and now prints before continuing, so a parse failure is no longer silently swallowed.
• TRY004 (1): RAGEngine._embed()'s type check now raises TypeError instead of ValueError (the correct exception for a type-validation failure) — updated the one test asserting on it (test_engine_embed_invalid_type) to match.
• EXE001 (1): scripts/run_eval.py had a shebang but wasn't executable; chmod +x to match, consistent with scripts/check_and_reindex.sh.
• F841 (4): four tests bound a mock to a name (mock_file, mock_pload, mock_retrieve ×2) and never asserted on it. Rather than delete the unused variable, added the assertion the surrounding test was clearly missing — each now verifies the mocked call actually happened, matching the pattern already used by sibling assertions in the same tests (e.g. mock_mkdirs.assert_called_once_with(...) right next to it).

Scoped # noqa: BLE001 — 17 sites, each with an inline reason, no blanket ignore:
Every one of these is except Exception at a deliberate error-isolation boundary — converting an arbitrary failure into a safe fallback (empty list, inline error string/token, HTTP 500, skip-and-continue) so one bad chunk/tool-step/subsystem/request doesn't crash a larger operation:

• api/routes/rag.py (3): engine-access wrapper, top-level /rag/query HTTP handler, SSE stream generator
• ingestion/doc_loader.py (1): per-file read during the indexing walk
• rag/engine.py (3): optional CrossEncoder load, LLM call, LLM streaming
• rag/query_router.py (4): per-source search (vector/graph/plugin) + streaming
• rag/tool_executor.py (4): per-step dispatch + per-tool search (vector/graph/plugin)
• scripts/build_index.py (1): per-chunk embed during batch indexing
• scripts/run_eval.py (1): per-query eval

Narrowing any of these to specific exception types would risk missing the failure modes the boundary exists to catch, defeating its purpose — that's why they're noqa'd with a reason rather than "fixed."

Verification

$ ruff check .
All checks passed!

$ pytest -q
199 passed in 0.5s

Confirmed 199 passed — same count as before this change — so none of the auto-fixes (import reordering, typing syntax) or manual fixes altered behavior.

CI

This should turn .github/workflows/ci.yml's "Lint & Test" job green again for the first time in several merges.

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⚠️ Not merging automatically per instructions — this diff touches 29 files (mostly mechanical, but worth a look given the volume). Waiting for review/confirmation before merge.

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🤖 Generated with Claude Code