fix: flush implicit transaction before BEGIN IMMEDIATE (#135)

[azizur100389]

Summary

• Fixes sqlite3.OperationalError: cannot start a transaction within a transaction when running code-review-graph update on a repo where git diff includes deleted files (sqlite3.OperationalError: cannot start a transaction within a transaction on update when git diff includes deleted files #135).
• Adds a guard in store_file_nodes_edges() to commit any pending implicit transaction before BEGIN IMMEDIATE.
• Adds 3 regression tests covering both incremental_update and full_build code paths.

Root Cause

Python's sqlite3 with default isolation_level="" auto-begins a DEFERRED transaction on the first DML. In incremental_update and full_build, remove_file_data() issues DELETE statements for deleted/stale files, silently opening an implicit transaction. The subsequent store_file_nodes_edges() then executes BEGIN IMMEDIATE inside that already-open transaction, which SQLite rejects.

Fix

Check self._conn.in_transaction before BEGIN IMMEDIATE and commit any pending implicit transaction. This preserves atomic replace semantics while being robust against prior implicit transaction state. The guard is a no-op when no implicit transaction is open.

Tests Added

• test_store_after_remove_no_transaction_error — direct GraphStore unit test
• test_incremental_deleted_and_modified_files — end-to-end incremental update with mixed deletes and modifications
• test_full_build_stale_files_then_parse — end-to-end full build with stale file purging

Test Plan

• All 3 new regression tests pass
• All existing test_graph.py and test_incremental.py tests pass (46/46)
• ruff check clean on all changed files

[tirth8205]

Closing in favor of #205 which was just merged and provides a more complete fix.

Your PR correctly identifies the problem and the in_transaction guard in store_file_nodes_edges() is the right instinct. The three regression tests (direct unit test, incremental update, full build) are thorough and well-structured.

However, PR #205 goes further:

1. Root cause elimination: sets isolation_level=None on all sqlite3.connect() calls — disabling implicit transactions project-wide so the guard becomes a true last-resort safety net rather than the primary defense.
2. Full incremental path: also commits after the deleted-file loop in incremental_update() (your incremental.py diff only patches full_build()).
3. Other connect() sites: your fix only touches graph.py, while fix: resolve SQLite transaction nesting errors (#135, #181) #205 also patches registry.py and embeddings.py.
4. Atomicity across batch ops: wraps store_flows(), store_communities(), and _compute_summaries blocks in explicit transactions.

Your end-to-end regression tests were valuable — they were the most comprehensive integration coverage among all the competing PRs. Thank you for the contribution.