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/db/migrations.ts

@@ -9,7 +9,7 @@ import { SqliteDatabase } from './sqlite-adapter';
 /**
  * Current schema version
  */
-export const CURRENT_SCHEMA_VERSION = 2;
+export const CURRENT_SCHEMA_VERSION = 3;
 
 /**
  * Migration definition
@@ -45,6 +45,15 @@ const migrations: Migration[] = [
       `);
     },
   },
+  {
+    version: 3,
+    description: 'Add lower(name) expression index for memory-efficient case-insensitive lookups',
+    up: (db) => {
+      db.exec(`
+        CREATE INDEX IF NOT EXISTS idx_nodes_lower_name ON nodes(lower(name));
+      `);
+    },
+  },
 ];
 
 /**