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>

package.json

@@ -1,12 +1,15 @@
 {
   "name": "@colbymchenry/codegraph",
-  "version": "0.1.0",
+  "version": "0.1.1",
   "description": "A local-first code intelligence system that builds a semantic knowledge graph from any codebase",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
   "bin": {
     "codegraph": "./dist/bin/codegraph.js"
   },
+  "files": [
+    "dist"
+  ],
   "scripts": {
     "build": "tsc && npm run copy-assets",
     "copy-assets": "cp -r src/extraction/queries dist/extraction/ && cp src/db/schema.sql dist/db/",
@@ -14,6 +17,8 @@
     "cli": "npm run build && node dist/bin/codegraph.js",
     "test": "vitest run",
     "test:watch": "vitest",
+    "test:eval": "vitest run __tests__/evaluation/",
+    "eval": "npm run build && npx tsx __tests__/evaluation/runner.ts",
     "clean": "rm -rf dist"
   },
   "keywords": [