Integration tests for annotation, audit, cache, and CallGraphFromTo tools

[data-douser]

Scope

Add client integration test fixtures and annotation mode to the test runner for annotation, audit, cache, and CallGraphFromTo tools.

Files

Client Integration Tests

• client/integration-tests/primitives/tools/annotation_{create,delete,list,search}/ — 4 annotation tool tests
• client/integration-tests/primitives/tools/audit_{add_notes,clear_repo,list_findings,store_findings}/ — 4 audit tool tests
• client/integration-tests/primitives/tools/query_results_cache_{clear,compare,lookup,retrieve}/ — 4 cache tool tests
• client/integration-tests/primitives/tools/codeql_query_run/{cpp,javascript,python}_call_graph_from_to_example1/ — 3 CallGraphFromTo tests
• client/integration-tests/workflows/mrva_finding_triage/ — 1 MRVA workflow test
• client/scripts/run-integration-tests.sh — annotation mode added

Extension Integration Tests

• extensions/vscode/test/suite/mcp-tool-e2e.integration.test.ts — annotation/audit/cache tool availability + MRVA e2e workflow

Independence

⚠️ Depends on #165 (SqliteStore + tools) — tests exercise the tools implemented there. Should merge after #165.

Parent: #163