feat: schema v2 migration, database performance, batch query methods

- Add provenance column on edges for tracking how edges were created
- Add project_metadata table for version/provenance tracking
- Make unresolved_refs file_path/language NOT NULL with defaults
- Add composite indexes for unresolved_refs and edges.provenance
- Update v2 migration to handle all new schema additions
- Record schema version on initialize to prevent re-migration
- Add dynamic prepared statement cache (getDynamicStmt) for varying SQL
- Add batch methods: getNodesByIds, getNodesByKinds, getFileHashMap, getFileSyncMap
- Add project metadata methods: getMetadata, setMetadata, getAllMetadata
- Optimize getStats to use single aggregate query
- Optimize getStaleFiles to use temporary table JOIN
- Add provenance parameter to getOutgoingEdges
- Add intent field to SearchOptions type

src/db/migrations.ts

@@ -29,11 +29,19 @@ interface Migration {
 const migrations: Migration[] = [
   {
     version: 2,
-    description: 'Add filePath and language to unresolved_refs for performance',
+    description: 'Add project metadata, provenance tracking, and unresolved ref context',
     up: (db) => {
       db.exec(`
-        ALTER TABLE unresolved_refs ADD COLUMN file_path TEXT;
-        ALTER TABLE unresolved_refs ADD COLUMN language TEXT;
+        CREATE TABLE IF NOT EXISTS project_metadata (
+          key TEXT PRIMARY KEY,
+          value TEXT NOT NULL,
+          updated_at INTEGER NOT NULL
+        );
+        ALTER TABLE unresolved_refs ADD COLUMN file_path TEXT NOT NULL DEFAULT '';
+        ALTER TABLE unresolved_refs ADD COLUMN language TEXT NOT NULL DEFAULT 'unknown';
+        ALTER TABLE edges ADD COLUMN provenance TEXT DEFAULT NULL;
+        CREATE INDEX IF NOT EXISTS idx_unresolved_file_path ON unresolved_refs(file_path);
+        CREATE INDEX IF NOT EXISTS idx_edges_provenance ON edges(provenance);
       `);
     },
   },