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/context/index.ts

@@ -26,15 +26,20 @@ import { logDebug, logWarn } from '../errors';
 
 /**
  * Default options for context building
+ *
+ * Tuned for minimal context usage while still providing useful results:
+ * - Fewer nodes and code blocks by default
+ * - Smaller code block size limit
+ * - Shallower traversal
  */
 const DEFAULT_BUILD_OPTIONS: Required<BuildContextOptions> = {
-  maxNodes: 50,
-  maxCodeBlocks: 10,
-  maxCodeBlockSize: 2000,
+  maxNodes: 20,           // Reduced from 50 - most tasks don't need 50 symbols
+  maxCodeBlocks: 5,       // Reduced from 10 - only show most relevant code
+  maxCodeBlockSize: 1500, // Reduced from 2000
   includeCode: true,
   format: 'markdown',
-  searchLimit: 5,
-  traversalDepth: 2,
+  searchLimit: 3,         // Reduced from 5 - fewer entry points
+  traversalDepth: 1,      // Reduced from 2 - shallower graph expansion
   minScore: 0.3,
 };
 
@@ -42,9 +47,9 @@ const DEFAULT_BUILD_OPTIONS: Required<BuildContextOptions> = {
  * Default options for finding relevant context
  */
 const DEFAULT_FIND_OPTIONS: Required<FindRelevantContextOptions> = {
-  searchLimit: 5,
-  traversalDepth: 2,
-  maxNodes: 50,
+  searchLimit: 3,        // Reduced from 5
+  traversalDepth: 1,     // Reduced from 2
+  maxNodes: 20,          // Reduced from 50
   minScore: 0.3,
   edgeKinds: [],
   nodeKinds: [],