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>

src/extraction/index.ts

@@ -65,13 +65,24 @@ export function hashContent(content: string): string {
  * Check if a path matches any glob pattern (simplified)
  */
 function matchesGlob(filePath: string, pattern: string): boolean {
-  // Convert glob to regex (simplified)
-  const regexStr = pattern
-    .replace(/\./g, '\\.')
-    .replace(/\*\*/g, '<<<GLOBSTAR>>>')
-    .replace(/\*/g, '[^/]*')
-    .replace(/<<<GLOBSTAR>>>/g, '.*')
-    .replace(/\?/g, '.');
+  // Convert glob to regex using placeholders to avoid conflicts
+  let regexStr = pattern;
+
+  // Replace glob patterns with placeholders first
+  regexStr = regexStr.replace(/\*\*\//g, '\x00GLOBSTAR_SLASH\x00');
+  regexStr = regexStr.replace(/\*\*/g, '\x00GLOBSTAR\x00');
+  regexStr = regexStr.replace(/\*/g, '\x00STAR\x00');
+  regexStr = regexStr.replace(/\?/g, '\x00QUESTION\x00');
+
+  // Escape regex special characters
+  regexStr = regexStr.replace(/[.+^${}()|[\]\\]/g, '\\$&');
+
+  // Replace placeholders with regex equivalents
+  regexStr = regexStr.replace(/\x00GLOBSTAR_SLASH\x00/g, '(?:.*/)?');  // **/ = zero or more dirs
+  regexStr = regexStr.replace(/\x00GLOBSTAR\x00/g, '.*');              // ** = anything
+  regexStr = regexStr.replace(/\x00STAR\x00/g, '[^/]*');               // * = anything except /
+  regexStr = regexStr.replace(/\x00QUESTION\x00/g, '.');               // ? = single char
+
   const regex = new RegExp(`^${regexStr}$`);
   return regex.test(filePath);
 }