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/auth.py

@@ -0,0 +1,79 @@
+"""Authentication service."""
+
+import hashlib
+import secrets
+from datetime import datetime
+from typing import Optional, Tuple
+
+from models import User
+from database import db
+from validation import validate_email, validate_password
+
+
+def hash_password(password: str) -> str:
+    """Hash a password for storage."""
+    salt = secrets.token_hex(16)
+    hash_obj = hashlib.sha256((password + salt).encode())
+    return f"{salt}:{hash_obj.hexdigest()}"
+
+
+def verify_password(password: str, password_hash: str) -> bool:
+    """Verify a password against its hash."""
+    salt, stored_hash = password_hash.split(":")
+    hash_obj = hashlib.sha256((password + salt).encode())
+    return hash_obj.hexdigest() == stored_hash
+
+
+def generate_token() -> str:
+    """Generate a secure random token."""
+    return secrets.token_urlsafe(32)
+
+
+class AuthService:
+    def __init__(self):
+        self.tokens: dict = {}
+
+    def register(self, email: str, password: str, name: str) -> Tuple[bool, str]:
+        """Register a new user."""
+        if not validate_email(email):
+            return False, "Invalid email format"
+
+        if not validate_password(password):
+            return False, "Password too weak"
+
+        if db.get_user_by_email(email):
+            return False, "Email already registered"
+
+        user = User(
+            id=generate_token(),
+            email=email,
+            name=name,
+            password_hash=hash_password(password),
+            created_at=datetime.now(),
+        )
+        db.create_user(user)
+        return True, user.id
+
+    def login(self, email: str, password: str) -> Optional[str]:
+        """Authenticate user and return token."""
+        user = db.get_user_by_email(email)
+        if not user:
+            return None
+
+        if not verify_password(password, user.password_hash):
+            return None
+
+        token = generate_token()
+        self.tokens[token] = user.id
+        return token
+
+    def logout(self, token: str) -> None:
+        """Invalidate a token."""
+        self.tokens.pop(token, None)
+
+    def get_user_id(self, token: str) -> Optional[str]:
+        """Get user ID from token."""
+        return self.tokens.get(token)
+
+
+auth_service = AuthService()