feat: Add database schema v3 with optimized node lookups and improved error handling

Adds expression index on lower(name) for memory-efficient case-insensitive searches, replacing in-memory caches that caused OOM on large codebases. Includes batched reference resolution, enhanced error reporting with detailed breakdown by error type, and improved CLI progress display for scanning phases.

src/types.ts

@@ -232,6 +232,9 @@ export interface ExtractionError {
   /** Error message */
   message: string;
 
+  /** File path where the error occurred */
+  filePath?: string;
+
   /** Line number if available */
   line?: number;