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/index.ts

@@ -367,7 +367,19 @@ export class CodeGraph {
    */
   async indexAll(options: IndexOptions = {}): Promise<IndexResult> {
     return this.indexMutex.withLock(async () => {
-      return this.orchestrator.indexAll(options.onProgress, options.signal);
+      const result = await this.orchestrator.indexAll(options.onProgress, options.signal);
+
+      // Resolve references to create call/import/extends edges
+      if (result.success && result.filesIndexed > 0) {
+        options.onProgress?.({
+          phase: 'resolving',
+          current: 0,
+          total: 1,
+        });
+        this.resolveReferences();
+      }
+
+      return result;
     });
   }
 
@@ -389,7 +401,14 @@ export class CodeGraph {
    */
   async sync(options: IndexOptions = {}): Promise<SyncResult> {
     return this.indexMutex.withLock(async () => {
-      return this.orchestrator.sync(options.onProgress);
+      const result = await this.orchestrator.sync(options.onProgress);
+
+      // Resolve references if files were updated
+      if (result.filesAdded > 0 || result.filesModified > 0) {
+        this.resolveReferences();
+      }
+
+      return result;
     });
   }