perf(db): batch node lookups, fix insertNode cache, auto-ANALYZE after writes

[mschreib28]

Summary\n\nThree DB-layer improvements bundled in one PR. All low-risk, high-leverage.\n\n### 1. Batch getNodesByIds — fix N+1 in graph traversal\n\nQueryBuilder.getNodesByIds(ids[]) returns Map<id, Node> in one SQL round-trip (chunked at 500 for SQLite param-limit safety; cache-aware so already-cached entries are served from memory and only the misses hit SQL).\n\nReplaces 9 N+1 loops in src/graph/traversal.ts:\n\n- getCallersRecursive / getCalleesRecursive\n- getTypeAncestors / getTypeDescendants\n- findUsages\n- getImpactRecursive (both inner loops: contains-children + dependents)\n- findPath BFS frontier\n- traverseBFS / traverseDFS neighbor expansion\n- getChildren\n\nEach previously did getNodeById per edge inside a loop; for a function with N callers at depth D, that was N^D point reads. Now: one IN-list query per traversal step. Expected 10–50× speedup on deep / fan-out-heavy traversals (impact analysis on popular utilities, call graphs of central modules).\n\n### 2. insertNode cache invalidation — fix correctness bug\n\nQueryBuilder.insertNode uses INSERT OR REPLACE INTO nodes. The LRU nodeCache was invalidated by updateNode and deleteNode but NOT by insertNode, so a re-indexed node (replacing a cached row) would still serve the pre-replace version on next getNodeById until LRU eviction pushed it out.\n\nNow invalidates nodeCache.delete(node.id) at the top of insertNode (after validation, before SQL — so failed-validation early-returns don't churn the cache).\n\n### 3. Auto-maintenance after bulk writes\n\nDatabaseConnection.runMaintenance() runs:\n\n- PRAGMA optimize — incremental ANALYZE; only re-analyzes tables whose row counts changed materially since the last ANALYZE. Without it, the SQLite query planner has zero statistics on freshly-bulk-loaded tables and can pick wrong indexes.\n- PRAGMA wal_checkpoint(PASSIVE) — fold WAL pages back into the main DB file so the WAL doesn't grow unboundedly between automatic checkpoints (which fire at 1000 pages).\n\nBoth non-blocking and silently swallowed on failure — best-effort, never load-bearing. Wired into indexAll (when files were indexed) and sync (when files changed). No-op when nothing happened.\n\n## Files changed\n\n| File | Change |\n|---|---|\n| src/db/queries.ts | Add getNodesByIds; invalidate cache in insertNode |\n| src/db/index.ts | Add runMaintenance() helper |\n| src/graph/traversal.ts | Replace 9 N+1 loops with batch lookups |\n| src/index.ts | Call runMaintenance after indexAll / sync |\n| __tests__/db-perf.test.ts (NEW) | 9 regression tests covering batch lookup, chunking, cache hits, cache invalidation, maintenance no-throw on closed DB |\n\n## Test plan\n\n- [x] npm test: 388/389 pass on macOS (one pre-existing fs.watch flake)\n- [x] npx tsc --noEmit clean\n- [x] Independent reviewer pass before pushing — APPROVE; one info finding addressed (getChildren was the 9th N+1 site, now batched too)\n\n🤖 Generated with Claude Code\n

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Copied from colbymchenry/codegraph#108