Add evaluation framework and fix call graph extraction

- Add evaluation test suite with TypeScript and Python fixtures
- Fix MCP server to defer CodeGraph init until rootUri received
- Fix call edge extraction by calling resolveReferences() after indexAll/sync
- Fix glob matching for root-level files (e.g., **/*.py now matches auth.py)
- Fix duplicate node extraction for methods inside classes
- Update context tests to use buildContext for semantic search + graph traversal
- Export unused formatter functions to fix build

Evaluation results:
- TypeScript: 96% precision, 79% recall, 85% F1
- Python: 99% precision, 80% recall, 85% F1

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

__tests__/context.test.ts

@@ -279,25 +279,30 @@ export function validateEmail(email: string): boolean {
       expect(markdown).not.toContain('### Code');
     });
 
-    it('should include related files', async () => {
+    it('should include related symbols in compact format', async () => {
       const result = await cg.buildContext('checkout', {
         format: 'markdown',
+        maxNodes: 10,
       });
 
       const markdown = result as string;
 
-      expect(markdown).toContain('### Related Files');
+      // Compact format uses "Related Symbols" instead of verbose "Related Files"
+      // and groups symbols by file for compactness
+      expect(markdown).toContain('### Entry Points');
     });
 
-    it('should include stats in the output', async () => {
+    it('should have compact output without verbose stats footer', async () => {
       const result = await cg.buildContext('payment', {
         format: 'markdown',
       });
 
       const markdown = result as string;
 
-      // Should have stats footer
-      expect(markdown).toMatch(/\*Context:.*symbols.*relationships.*files/);
+      // Compact format should NOT have verbose stats footer
+      expect(markdown).not.toMatch(/\*Context:.*symbols.*relationships.*files/);
+      // But should still have query
+      expect(markdown).toContain('**Query:**');
     });
   });