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/extraction/dfm-extractor.ts

@@ -39,6 +39,7 @@ export class DfmExtractor {
       this.errors.push({
         message: `DFM extraction error: ${error instanceof Error ? error.message : String(error)}`,
         severity: 'error',
+        code: 'parse_error',
       });
     }