fix: resolve SQLite transaction bugs, FTS5 sync, and atomic operations

[murilloimparavel]

Summary

Fixes multiple SQLite transaction management issues that cause cannot start a transaction within a transaction errors and potential data corruption:

• BEGIN IMMEDIATE conflict (graph.py): Add in_transaction guard before BEGIN IMMEDIATE to prevent errors when implicit transactions are left open by prior DML operations
• FTS5 content sync (search.py): Recreate FTS5 table with content='nodes' and use INSERT INTO nodes_fts(nodes_fts) VALUES('rebuild') for proper content-sync population (was creating standalone table disconnected from nodes)
• Atomic batch operations (flows.py, communities.py): Wrap DELETE + INSERT loops in BEGIN IMMEDIATE / try / COMMIT / except ROLLBACK to prevent partial writes on crash
• Missing rollback on error (tools/build.py): Add store.rollback() in post-processing except blocks to prevent lingering transactions that corrupt the DB on next run
• Public rollback API (graph.py): Expose GraphStore.rollback() method instead of accessing _conn directly
• Diagnostic logging: Add logger.warning() before silent rollbacks in transaction guards for debuggability

Reproduction

The cannot start a transaction within a transaction error occurs when:

1. store_file_nodes_edges() calls BEGIN IMMEDIATE while a prior operation (e.g., set_metadata, upsert_node) left an implicit Python sqlite3 transaction open
2. Post-processing steps (signatures, FTS, flows, communities) fail partially without rollback, leaving the DB in a dirty state for the next build

Test plan

• Full rebuild on monorepo with 8,352 nodes, 50,259 edges — zero transaction errors
• Verified FTS5 content sync works correctly after rebuild
• Verified flows (1,185) and communities (605) populated correctly
• Verified rollback logging appears when uncommitted transactions are detected
• All 29 CLI functional tests passing

🤖 Generated with Claude Code

[tirth8205]

This fixes a real and impactful SQLite transaction nesting bug (closes #135, #110). The in_transaction guard and atomic batch wrapping are the right approach.

Please rebase on latest main and add test coverage for the transaction nesting scenario (e.g., update with deleted files in diff). Once done, this is ready to merge.

[tirth8205]

Review: PR #94 — fix: resolve SQLite transaction bugs, FTS5 sync, and atomic operations

This is a high-quality, focused bug fix PR. The core fixes are correct:

• The in_transaction guard before BEGIN IMMEDIATE directly prevents the 'cannot start a transaction within a transaction' OperationalError
• Using content='nodes', content_rowid='rowid' with INSERT INTO nodes_fts(nodes_fts) VALUES('rebuild') is the correct FTS5 content-sync pattern
• Wrapping the DELETE + INSERT loops in BEGIN IMMEDIATE / ROLLBACK in flows.py and communities.py prevents partial writes
• Adding store.rollback() in the except blocks of tools/build.py prevents lingering transactions
• Exposing GraphStore.rollback() as a public API is the right abstraction

One issue to fix:
There is a duplicate logger = logging.getLogger(__name__) declaration in search.py (lines 16 and 19 in the diff). This is a minor bug but will generate a lint warning. Please remove the duplicate.

Rebase status: The owner requested a rebase and test coverage for the transaction nesting scenario. The author rebased (comment from April 8). Please confirm the test for the nesting scenario was added — the diff shown does not include a test for concurrent store_file_nodes_edges calls leaving an open transaction.

Merge order note: The owner stated this should merge before #95 (which overlaps on post-processing). Please ensure rebase is current with main and CI passes.

Verdict: Nearly ready to merge. Fix the duplicate logger declaration, confirm CI passes, and this is mergeable.

[tirth8205]

Update: Merge conflict detected. GitHub reports this PR has merge conflicts with main (mergeStateStatus: DIRTY). Despite the author rebasing on April 8, there have been additional merges since then. Please rebase again on the current main branch. Once conflicts are resolved, fix the duplicate logger in search.py, and CI passes, this is ready to merge.

[murilloimparavel]

Rebased on latest main and addressed reviewer feedback:

• Added comprehensive transaction robustness tests (tests/test_transactions.py) covering nested transaction guards, atomic batch operations, and rollback-on-failure scenarios.
• Added FTS5 content sync tests (tests/test_fts_sync.py) to verify proper population of the virtual table from the nodes table.
• Removed the duplicate logger declaration in search.py.
• Verified that all 7 new tests pass and confirmed no regressions in existing CLI tests.
  Ready for final review.