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/index.ts

@@ -52,6 +52,14 @@ export class DatabaseConnection {
     const schema = fs.readFileSync(schemaPath, 'utf-8');
     db.exec(schema);
 
+    // Record current schema version so migrations aren't re-applied on open
+    const currentVersion = getCurrentVersion(db);
+    if (currentVersion < CURRENT_SCHEMA_VERSION) {
+      db.prepare(
+        'INSERT OR IGNORE INTO schema_versions (version, applied_at, description) VALUES (?, ?, ?)'
+      ).run(CURRENT_SCHEMA_VERSION, Date.now(), 'Initial schema includes all migrations');
+    }
+
     return new DatabaseConnection(db, dbPath);
   }