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/database.py

@@ -0,0 +1,54 @@
+"""Database operations."""
+
+from typing import Optional, List, Dict
+from models import User, Task, Project
+
+
+class Database:
+    def __init__(self):
+        self.users: Dict[str, User] = {}
+        self.tasks: Dict[str, Task] = {}
+        self.projects: Dict[str, Project] = {}
+
+    def get_user(self, user_id: str) -> Optional[User]:
+        return self.users.get(user_id)
+
+    def get_user_by_email(self, email: str) -> Optional[User]:
+        for user in self.users.values():
+            if user.email == email:
+                return user
+        return None
+
+    def create_user(self, user: User) -> None:
+        self.users[user.id] = user
+
+    def get_task(self, task_id: str) -> Optional[Task]:
+        return self.tasks.get(task_id)
+
+    def get_user_tasks(self, user_id: str) -> List[Task]:
+        return [t for t in self.tasks.values() if t.user_id == user_id]
+
+    def create_task(self, task: Task) -> None:
+        self.tasks[task.id] = task
+
+    def update_task(self, task_id: str, **updates) -> Optional[Task]:
+        task = self.tasks.get(task_id)
+        if task:
+            for key, value in updates.items():
+                setattr(task, key, value)
+        return task
+
+    def delete_task(self, task_id: str) -> bool:
+        if task_id in self.tasks:
+            del self.tasks[task_id]
+            return True
+        return False
+
+    def get_project(self, project_id: str) -> Optional[Project]:
+        return self.projects.get(project_id)
+
+    def create_project(self, project: Project) -> None:
+        self.projects[project.id] = project
+
+
+db = Database()