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.

__tests__/foundation.test.ts

@@ -317,7 +317,7 @@ describe('Database Connection', () => {
 
     const version = db.getSchemaVersion();
     expect(version).not.toBeNull();
-    expect(version?.version).toBe(2);
+    expect(version?.version).toBe(3);
 
     db.close();
   });