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/schema.sql

@@ -11,8 +11,6 @@ CREATE TABLE IF NOT EXISTS schema_versions (
 -- Insert initial version
 INSERT INTO schema_versions (version, applied_at, description)
 VALUES (1, strftime('%s', 'now') * 1000, 'Initial schema');
-INSERT INTO schema_versions (version, applied_at, description)
-VALUES (2, strftime('%s', 'now') * 1000, 'Add filePath and language to unresolved_refs');
 
 -- =============================================================================
 -- Core Tables
@@ -51,6 +49,7 @@ CREATE TABLE IF NOT EXISTS edges (
     metadata TEXT, -- JSON object
     line INTEGER,
     col INTEGER,
+    provenance TEXT DEFAULT NULL,
     FOREIGN KEY (source) REFERENCES nodes(id) ON DELETE CASCADE,
     FOREIGN KEY (target) REFERENCES nodes(id) ON DELETE CASCADE
 );
@@ -75,9 +74,9 @@ CREATE TABLE IF NOT EXISTS unresolved_refs (
     reference_kind TEXT NOT NULL,
     line INTEGER NOT NULL,
     col INTEGER NOT NULL,
-    file_path TEXT,
-    language TEXT,
     candidates TEXT, -- JSON array
+    file_path TEXT NOT NULL DEFAULT '',
+    language TEXT NOT NULL DEFAULT 'unknown',
     FOREIGN KEY (from_node_id) REFERENCES nodes(id) ON DELETE CASCADE
 );
 
@@ -136,6 +135,9 @@ CREATE INDEX IF NOT EXISTS idx_files_modified_at ON files(modified_at);
 -- Unresolved refs indexes
 CREATE INDEX IF NOT EXISTS idx_unresolved_from_node ON unresolved_refs(from_node_id);
 CREATE INDEX IF NOT EXISTS idx_unresolved_name ON unresolved_refs(reference_name);
+CREATE INDEX IF NOT EXISTS idx_unresolved_file_path ON unresolved_refs(file_path);
+CREATE INDEX IF NOT EXISTS idx_unresolved_from_name ON unresolved_refs(from_node_id, reference_name);
+CREATE INDEX IF NOT EXISTS idx_edges_provenance ON edges(provenance);
 
 -- =============================================================================
 -- Vector Storage (for future semantic search)
@@ -152,3 +154,10 @@ CREATE TABLE IF NOT EXISTS vectors (
 );
 
 CREATE INDEX IF NOT EXISTS idx_vectors_model ON vectors(model);
+
+-- Project metadata for version/provenance tracking
+CREATE TABLE IF NOT EXISTS project_metadata (
+    key TEXT PRIMARY KEY,
+    value TEXT NOT NULL,
+    updated_at INTEGER NOT NULL
+);