fix: transaction safety, resource cleanup, and truncation signaling (#258, #259, #260, #261)

[azizur100389]

Summary

Four reliability hardening fixes that improve crash safety, resource cleanup, and API transparency across the graph pipeline. 8 files changed, +206 / -25, 6 new regression tests.

Closes #258, closes #259, closes #260, closes #261.

---

Fix 1 — Wrap incremental_trace_flows DELETEs in a transaction (#258)

File: code_review_graph/flows.py:499-502

The DELETE loop deleted flow_memberships and flows rows one at a time without an explicit transaction. A crash mid-loop could leave orphaned flow_memberships rows pointing at deleted flows.

Fix: Wrap in BEGIN IMMEDIATE / COMMIT / ROLLBACK, matching the pattern already used by store_flows at line 406. Includes an in_transaction guard to flush any implicit transaction first.

Test: test_incremental_trace_flows_delete_is_atomic — verifies zero orphaned memberships after an incremental re-trace.

Fix 2 — Atomic FTS index rebuild (#259)

File: code_review_graph/search.py:39-54

rebuild_fts_index performed DROP, CREATE, and INSERT across three separate statements with commits between them. A crash after DROP but before CREATE would leave the DB without an FTS table entirely.

Fix: Wrap the entire DROP + CREATE + INSERT sequence in a single BEGIN IMMEDIATE transaction so the operation is all-or-nothing.

Test: test_fts_rebuild_is_atomic — verifies double-rebuild leaves the table intact and queryable.

Fix 3 — EmbeddingStore context manager support (#260)

File: code_review_graph/embeddings.py:391+

EmbeddingStore opens a SQLite connection in __init__ but did not implement __enter__ / __exit__. If an exception occurred during usage before close() was called, the connection leaked.

Fix: Add __enter__ and __exit__ methods following the same pattern as GraphStore (graph.py:154-157).

Tests: test_supports_context_manager, test_context_manager_closes_on_exception.

Fix 4 — Truncation signal for find_dependents (#261)

File: code_review_graph/incremental.py:434-465

When find_dependents hit _MAX_DEPENDENT_FILES (500), it truncated the result and logged a warning, but the caller received a plain list with no indication that it was incomplete.

Fix: Introduce DependentList — a transparent list subclass with a .truncated boolean attribute. Existing callers that iterate, len(), or slice continue to work unchanged; only callers that specifically check .truncated benefit from the signal.

Tests: test_truncated_flag_set_when_capped (600 deps → truncated=True), test_truncated_flag_false_when_not_capped (small chain → truncated=False).

---

Files changed (8 files, +206 / -25)

File	Change
code_review_graph/flows.py	Transaction wrap around DELETE loop
code_review_graph/search.py	Atomic FTS rebuild
code_review_graph/embeddings.py	__enter__/__exit__ on EmbeddingStore
code_review_graph/incremental.py	DependentList with .truncated flag
tests/test_flows.py	Orphan membership check
tests/test_search.py	Double-rebuild atomicity test
tests/test_embeddings.py	Context manager tests
tests/test_incremental.py	Truncation flag tests

Test results

Stage	Result
New targeted tests	6/6 passed
All affected test files	137 passed, 3 pre-existing failures (covered by parallel PRs #274/#276)
Full suite	784 passed, 8 pre-existing Windows failures (all covered by parallel PRs)
ruff check on all 8 changed files	clean
mypy on all 4 changed source files	clean

Zero regressions. All fixes follow established patterns already used elsewhere in the codebase.