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__/evaluation/fixtures/python-project/tasks.py

@@ -0,0 +1,72 @@
+"""Task management service."""
+
+from datetime import datetime
+from typing import Optional, List
+
+from models import Task
+from database import db
+from auth import auth_service, generate_token
+from validation import validate_task_title
+
+
+class TaskService:
+    def create_task(
+        self, token: str, title: str, description: Optional[str] = None
+    ) -> Optional[Task]:
+        """Create a new task."""
+        user_id = auth_service.get_user_id(token)
+        if not user_id:
+            return None
+
+        if not validate_task_title(title):
+            return None
+
+        task = Task(
+            id=generate_token(),
+            user_id=user_id,
+            title=title,
+            description=description,
+            completed=False,
+            created_at=datetime.now(),
+        )
+        db.create_task(task)
+        return task
+
+    def get_task(self, token: str, task_id: str) -> Optional[Task]:
+        """Get a task by ID."""
+        user_id = auth_service.get_user_id(token)
+        if not user_id:
+            return None
+
+        task = db.get_task(task_id)
+        if task and task.user_id == user_id:
+            return task
+        return None
+
+    def get_user_tasks(self, token: str) -> List[Task]:
+        """Get all tasks for the authenticated user."""
+        user_id = auth_service.get_user_id(token)
+        if not user_id:
+            return []
+
+        return db.get_user_tasks(user_id)
+
+    def complete_task(self, token: str, task_id: str) -> bool:
+        """Mark a task as completed."""
+        task = self.get_task(token, task_id)
+        if not task:
+            return False
+
+        db.update_task(task_id, completed=True, completed_at=datetime.now())
+        return True
+
+    def delete_task(self, token: str, task_id: str) -> bool:
+        """Delete a task."""
+        task = self.get_task(token, task_id)
+        if not task:
+            return False
+
+        return db.delete_task(task_id)
+
+
+task_service = TaskService()