mcp-code-indexer 3.1.4__py3-none-any.whl → 3.1.6__py3-none-any.whl

mcp_code_indexer/server/mcp_server.py

@@ -6,7 +6,6 @@ for file description management tools.
 """
 
 import asyncio
-import hashlib
 import html
 import json
 import logging
@@ -14,7 +13,7 @@ import re
 import uuid
 from datetime import datetime
 from pathlib import Path
-from typing import Any, Dict, List, Optional, Set
+from typing import Any, Dict, List, Optional
 
 from mcp import types
 from mcp.server import Server
@@ -25,12 +24,15 @@ from mcp_code_indexer.database.database import DatabaseManager
 from mcp_code_indexer.file_scanner import FileScanner
 from mcp_code_indexer.token_counter import TokenCounter
 from mcp_code_indexer.database.models import (
-    Project, FileDescription, CodebaseOverview, SearchResult,
-    CodebaseSizeInfo, FolderNode, FileNode, ProjectOverview,
-    WordFrequencyResult
+    Project,
+    FileDescription,
+    ProjectOverview,
+)
+from mcp_code_indexer.error_handler import setup_error_handling
+from mcp_code_indexer.middleware.error_middleware import (
+    create_tool_middleware,
+    AsyncTaskManager,
 )
-from mcp_code_indexer.error_handler import setup_error_handling, ErrorHandler
-from mcp_code_indexer.middleware.error_middleware import create_tool_middleware, AsyncTaskManager
 from mcp_code_indexer.logging_config import get_logger
 
 
@@ -40,11 +42,11 @@ logger = logging.getLogger(__name__)
 class MCPCodeIndexServer:
     """
     MCP Code Index Server.
-    
+
     Provides file description tracking and codebase navigation tools
     through the Model Context Protocol.
     """
-    
+
     def __init__(
         self,
         token_limit: int = 32000,
@@ -57,11 +59,11 @@ class MCPCodeIndexServer:
         health_check_interval: float = 30.0,
         retry_min_wait: float = 0.1,
         retry_max_wait: float = 2.0,
-        retry_jitter: float = 0.2
+        retry_jitter: float = 0.2,
     ):
         """
         Initialize the MCP Code Index Server.
-        
+
         Args:
             token_limit: Maximum tokens before recommending search over overview
             db_path: Path to SQLite database
@@ -78,7 +80,7 @@ class MCPCodeIndexServer:
         self.token_limit = token_limit
         self.db_path = db_path or Path.home() / ".mcp-code-index" / "tracker.db"
         self.cache_dir = cache_dir or Path.home() / ".mcp-code-index" / "cache"
-        
+
         # Store database configuration
         self.db_config = {
             "pool_size": db_pool_size,
@@ -88,12 +90,12 @@ class MCPCodeIndexServer:
             "health_check_interval": health_check_interval,
             "retry_min_wait": retry_min_wait,
             "retry_max_wait": retry_max_wait,
-            "retry_jitter": retry_jitter
+            "retry_jitter": retry_jitter,
         }
-        
+
         # Initialize components
         self.db_manager = DatabaseManager(
-            db_path=self.db_path, 
+            db_path=self.db_path,
             pool_size=db_pool_size,
             retry_count=db_retry_count,
             timeout=db_timeout,
@@ -101,58 +103,58 @@ class MCPCodeIndexServer:
             health_check_interval=health_check_interval,
             retry_min_wait=retry_min_wait,
             retry_max_wait=retry_max_wait,
-            retry_jitter=retry_jitter
+            retry_jitter=retry_jitter,
         )
         self.token_counter = TokenCounter(token_limit)
-        
+
         # Setup error handling
         self.logger = get_logger(__name__)
         self.error_handler = setup_error_handling(self.logger)
         self.middleware = create_tool_middleware(self.error_handler)
         self.task_manager = AsyncTaskManager(self.error_handler)
-        
+
         # Create MCP server
         self.server = Server("mcp-code-indexer")
-        
+
         # Register handlers
         self._register_handlers()
-        
+
         # Add debug logging for server events
         self.logger.debug("MCP server instance created and handlers registered")
-        
+
         self.logger.info(
-            "MCP Code Index Server initialized", 
-            extra={"structured_data": {"initialization": {"token_limit": token_limit}}}
+            "MCP Code Index Server initialized",
+            extra={"structured_data": {"initialization": {"token_limit": token_limit}}},
         )
-    
+
     def _clean_html_entities(self, text: str) -> str:
         """
         Clean HTML entities from text to prevent encoding issues.
-        
+
         Args:
             text: Text that may contain HTML entities
-            
+
         Returns:
             Text with HTML entities decoded to proper characters
         """
         if not text:
             return text
-        
+
         # Decode HTML entities like < > & etc.
         return html.unescape(text)
-    
+
     def _clean_arguments(self, arguments: Dict[str, Any]) -> Dict[str, Any]:
         """
         Clean HTML entities from all text arguments.
-        
+
         Args:
             arguments: Dictionary of arguments to clean
-            
+
         Returns:
             Dictionary with HTML entities decoded in all string values
         """
         cleaned = {}
-        
+
         for key, value in arguments.items():
             if isinstance(value, str):
                 cleaned[key] = self._clean_html_entities(value)
@@ -168,19 +170,19 @@ class MCPCodeIndexServer:
             else:
                 # Pass through other types unchanged
                 cleaned[key] = value
-        
+
         return cleaned
-    
+
     def _parse_json_robust(self, json_str: str) -> Dict[str, Any]:
         """
         Parse JSON with automatic repair for common issues.
-        
+
         Args:
             json_str: JSON string that may have formatting issues
-            
+
         Returns:
             Parsed JSON dictionary
-            
+
         Raises:
             ValueError: If JSON cannot be parsed even after repair attempts
         """
@@ -189,264 +191,474 @@ class MCPCodeIndexServer:
             return json.loads(json_str)
         except json.JSONDecodeError as original_error:
             logger.warning(f"Initial JSON parse failed: {original_error}")
-            
+
             # Try to repair common issues
             repaired = json_str
-            
+
             # Fix 1: Quote unquoted URLs and paths
             # Look for patterns like: "key": http://... or "key": /path/...
             url_pattern = r'("[\w]+"):\s*([a-zA-Z][a-zA-Z0-9+.-]*://[^\s,}]+|/[^\s,}]*)'
             repaired = re.sub(url_pattern, r'\1: "\2"', repaired)
-            
+
             # Fix 2: Quote unquoted boolean-like strings
-            # Look for: "key": true-ish-string or "key": false-ish-string  
-            bool_pattern = r'("[\w]+"):\s*([a-zA-Z][a-zA-Z0-9_-]*[a-zA-Z0-9])(?=\s*[,}])'
+            # Look for: "key": true-ish-string or "key": false-ish-string
+            bool_pattern = (
+                r'("[\w]+"):\s*([a-zA-Z][a-zA-Z0-9_-]*[a-zA-Z0-9])(?=\s*[,}])'
+            )
             repaired = re.sub(bool_pattern, r'\1: "\2"', repaired)
-            
+
             # Fix 3: Remove trailing commas
-            repaired = re.sub(r',(\s*[}\]])', r'\1', repaired)
-            
+            repaired = re.sub(r",(\s*[}\]])", r"\1", repaired)
+
             # Fix 4: Ensure proper string quoting for common unquoted values
             # Handle cases like: "key": value (where value should be "value")
             unquoted_pattern = r'("[\w]+"):\s*([a-zA-Z0-9_-]+)(?=\s*[,}])'
             repaired = re.sub(unquoted_pattern, r'\1: "\2"', repaired)
-            
+
             try:
                 result = json.loads(repaired)
-                logger.info(f"Successfully repaired JSON. Original: {json_str[:100]}...")
+                logger.info(
+                    f"Successfully repaired JSON. Original: {json_str[:100]}..."
+                )
                 logger.info(f"Repaired: {repaired[:100]}...")
                 return result
             except json.JSONDecodeError as repair_error:
                 logger.error(f"JSON repair failed. Original: {json_str}")
                 logger.error(f"Repaired attempt: {repaired}")
-                raise ValueError(f"Could not parse JSON even after repair attempts. Original error: {original_error}, Repair error: {repair_error}")
-    
+                raise ValueError(
+                    f"Could not parse JSON even after repair attempts. "
+                    f"Original error: {original_error}, Repair error: {repair_error}"
+                )
+
     async def initialize(self) -> None:
         """Initialize database and other resources."""
         await self.db_manager.initialize()
         logger.info("Server initialized successfully")
-    
+
     def _register_handlers(self) -> None:
         """Register MCP tool and resource handlers."""
-        
+
         @self.server.list_tools()
         async def list_tools() -> List[types.Tool]:
             """Return list of available tools."""
             return [
                 types.Tool(
                     name="get_file_description",
-                    description="Retrieves the stored description for a specific file in a codebase. Use this to quickly understand what a file contains without reading its full contents.",
+                    description=(
+                        "Retrieves the stored description for a specific file in a "
+                        "codebase. Use this to quickly understand what a file "
+                        "contains without reading its full contents."
+                    ),
                     inputSchema={
                         "type": "object",
                         "properties": {
                             "projectName": {
                                 "type": "string",
-                                "description": "The name of the project"
+                                "description": "The name of the project",
                             },
                             "folderPath": {
-                                "type": "string", 
-                                "description": "Absolute path to the project folder on disk"
+                                "type": "string",
+                                "description": (
+                                    "Absolute path to the project folder on disk"
+                                ),
                             },
-
-
                             "filePath": {
                                 "type": "string",
-                                "description": "Relative path to the file from project root"
-                            }
+                                "description": (
+                                    "Relative path to the file from project root"
+                                ),
+                            },
                         },
                         "required": ["projectName", "folderPath", "filePath"],
-                        "additionalProperties": False
-                    }
+                        "additionalProperties": False,
+                    },
                 ),
                 types.Tool(
                     name="update_file_description",
-                    description="Creates or updates the description for a file. Use this after analyzing a file's contents to store a detailed summary.",
+                    description=(
+                        "Creates or updates the description for a file. Use this "
+                        "after analyzing a file's contents to store a detailed summary."
+                    ),
                     inputSchema={
                         "type": "object",
                         "properties": {
-                            "projectName": {"type": "string", "description": "The name of the project"},
-                            "folderPath": {"type": "string", "description": "Absolute path to the project folder on disk"},
-
-                            "filePath": {"type": "string", "description": "Relative path to the file from project root"},
-                            "description": {"type": "string", "description": "Detailed description of the file's contents"},
-                            "fileHash": {"type": "string", "description": "SHA-256 hash of the file contents (optional)"}
+                            "projectName": {
+                                "type": "string",
+                                "description": "The name of the project",
+                            },
+                            "folderPath": {
+                                "type": "string",
+                                "description": (
+                                    "Absolute path to the project folder on disk"
+                                ),
+                            },
+                            "filePath": {
+                                "type": "string",
+                                "description": (
+                                    "Relative path to the file from project root"
+                                ),
+                            },
+                            "description": {
+                                "type": "string",
+                                "description": (
+                                    "Detailed description of the file's contents"
+                                ),
+                            },
+                            "fileHash": {
+                                "type": "string",
+                                "description": (
+                                    "SHA-256 hash of the file contents (optional)"
+                                ),
+                            },
                         },
-                        "required": ["projectName", "folderPath", "filePath", "description"],
-                        "additionalProperties": False
-                    }
+                        "required": [
+                            "projectName",
+                            "folderPath",
+                            "filePath",
+                            "description",
+                        ],
+                        "additionalProperties": False,
+                    },
                 ),
                 types.Tool(
                     name="check_codebase_size",
-                    description="Checks the total token count of a codebase's file structure and descriptions. Returns whether the codebase is 'large' and recommends using search instead of the full overview.",
+                    description=(
+                        "Checks the total token count of a codebase's file structure "
+                        "and descriptions. Returns whether the codebase is 'large' "
+                        "and recommends using search instead of the full overview."
+                    ),
                     inputSchema={
                         "type": "object",
                         "properties": {
-                            "projectName": {"type": "string", "description": "The name of the project"},
-                            "folderPath": {"type": "string", "description": "Absolute path to the project folder on disk"},
-
-                            "tokenLimit": {"type": "integer", "description": "Optional token limit override (defaults to server configuration)"}
+                            "projectName": {
+                                "type": "string",
+                                "description": "The name of the project",
+                            },
+                            "folderPath": {
+                                "type": "string",
+                                "description": (
+                                    "Absolute path to the project folder on disk"
+                                ),
+                            },
+                            "tokenLimit": {
+                                "type": "integer",
+                                "description": (
+                                    "Optional token limit override "
+                                    "(defaults to server configuration)"
+                                ),
+                            },
                         },
                         "required": ["projectName", "folderPath"],
-                        "additionalProperties": False
-                    }
+                        "additionalProperties": False,
+                    },
                 ),
                 types.Tool(
                     name="find_missing_descriptions",
-                    description="Scans the project folder to find files that don't have descriptions yet. Use update_file_description to add descriptions for individual files.",
+                    description=(
+                        "Scans the project folder to find files that don't have "
+                        "descriptions yet. Use update_file_description to add "
+                        "descriptions for individual files."
+                    ),
                     inputSchema={
                         "type": "object",
                         "properties": {
-                            "projectName": {"type": "string", "description": "The name of the project"},
-                            "folderPath": {"type": "string", "description": "Absolute path to the project folder on disk"},
-
-                            "limit": {"type": "integer", "description": "Maximum number of missing files to return (optional)"}
+                            "projectName": {
+                                "type": "string",
+                                "description": "The name of the project",
+                            },
+                            "folderPath": {
+                                "type": "string",
+                                "description": (
+                                    "Absolute path to the project folder on disk"
+                                ),
+                            },
+                            "limit": {
+                                "type": "integer",
+                                "description": (
+                                    "Maximum number of missing files to return "
+                                    "(optional)"
+                                ),
+                            },
                         },
                         "required": ["projectName", "folderPath"],
-                        "additionalProperties": False
-                    }
+                        "additionalProperties": False,
+                    },
                 ),
                 types.Tool(
                     name="search_descriptions",
-                    description="Searches through all file descriptions in a project to find files related to specific functionality. Use this for large codebases instead of loading the entire structure. Always start with the fewest terms possible (1 to 3 words AT MOST); if the tool returns a lot of results (more than 20) or the results are not relevant, then narrow it down by increasing the number of search words one at a time and calling the tool again. Start VERY broad, then narrow the focus only if needed!",
+                    description=(
+                        "Searches through all file descriptions in a project to find "
+                        "files related to specific functionality. Use this for large "
+                        "codebases instead of loading the entire structure. Always "
+                        "start with the fewest terms possible (1 to 3 words AT MOST); "
+                        "if the tool returns a lot of results (more than 20) or the "
+                        "results are not relevant, then narrow it down by increasing "
+                        "the number of search words one at a time and calling the tool "
+                        "again. Start VERY broad, then narrow the focus only if needed!"
+                    ),
                     inputSchema={
                         "type": "object",
                         "properties": {
-                            "projectName": {"type": "string", "description": "The name of the project"},
-                            "folderPath": {"type": "string", "description": "Absolute path to the project folder on disk"},
-
-                            "query": {"type": "string", "description": "Search query (e.g., 'authentication middleware', 'database models')"},
-                            "maxResults": {"type": "integer", "default": 20, "description": "Maximum number of results to return"}
+                            "projectName": {
+                                "type": "string",
+                                "description": "The name of the project",
+                            },
+                            "folderPath": {
+                                "type": "string",
+                                "description": (
+                                    "Absolute path to the project folder on disk"
+                                ),
+                            },
+                            "query": {
+                                "type": "string",
+                                "description": (
+                                    "Search query (e.g., 'authentication middleware', "
+                                    "'database models')"
+                                ),
+                            },
+                            "maxResults": {
+                                "type": "integer",
+                                "default": 20,
+                                "description": "Maximum number of results to return",
+                            },
                         },
                         "required": ["projectName", "folderPath", "query"],
-                        "additionalProperties": False
-                    }
+                        "additionalProperties": False,
+                    },
                 ),
                 types.Tool(
                     name="get_all_descriptions",
-                    description="Returns the complete file-by-file structure of a codebase with individual descriptions for each file. For large codebases, consider using get_codebase_overview for a condensed summary instead.",
+                    description=(
+                        "Returns the complete file-by-file structure of a codebase "
+                        "with individual descriptions for each file. For large "
+                        "codebases, consider using get_codebase_overview for a "
+                        "condensed summary instead."
+                    ),
                     inputSchema={
                         "type": "object",
                         "properties": {
-                            "projectName": {"type": "string", "description": "The name of the project"},
-                            "folderPath": {"type": "string", "description": "Absolute path to the project folder on disk"}
+                            "projectName": {
+                                "type": "string",
+                                "description": "The name of the project",
+                            },
+                            "folderPath": {
+                                "type": "string",
+                                "description": (
+                                    "Absolute path to the project folder on disk"
+                                ),
+                            },
                         },
                         "required": ["projectName", "folderPath"],
-                        "additionalProperties": False
-                    }
+                        "additionalProperties": False,
+                    },
                 ),
                 types.Tool(
                     name="get_codebase_overview",
-                    description="Returns a condensed, interpretive overview of the entire codebase. This is a single comprehensive narrative that captures the architecture, key components, relationships, and design patterns. Unlike get_all_descriptions which lists every file, this provides a holistic view suitable for understanding the codebase's structure and purpose. If no overview exists, returns empty string.",
+                    description=(
+                        "Returns a condensed, interpretive overview of the entire "
+                        "codebase. This is a single comprehensive narrative that "
+                        "captures the architecture, key components, relationships, "
+                        "and design patterns. Unlike get_all_descriptions which "
+                        "lists every file, this provides a holistic view suitable "
+                        "for understanding the codebase's structure and purpose. "
+                        "If no overview exists, returns empty string."
+                    ),
                     inputSchema={
                         "type": "object",
                         "properties": {
-                            "projectName": {"type": "string", "description": "The name of the project"},
-                            "folderPath": {"type": "string", "description": "Absolute path to the project folder on disk"}
+                            "projectName": {
+                                "type": "string",
+                                "description": "The name of the project",
+                            },
+                            "folderPath": {
+                                "type": "string",
+                                "description": (
+                                    "Absolute path to the project folder on disk"
+                                ),
+                            },
                         },
                         "required": ["projectName", "folderPath"],
-                        "additionalProperties": False
-                    }
+                        "additionalProperties": False,
+                    },
                 ),
                 types.Tool(
                     name="update_codebase_overview",
-                    description="""Creates a concise codebase overview for AI agents. Focus on essential navigation and context in 3500-7000 words. Include: (1) One-paragraph system summary - what it does and its core purpose, (2) Directory tree with one-line descriptions for each major folder, (3) Key architectural patterns (e.g., MVC, microservices, event-driven) in 2-3 sentences, (4) Critical file locations (entry points, config, main business logic), (5) Essential conventions (naming, file organization, error handling), (6) Important gotchas or non-obvious connections. Keep it scannable and action-oriented.
-
-Example:
-
-````
-## System Summary
-E-commerce platform handling product catalog, orders, and payments with React frontend and Node.js API.
-
-## Directory Structure
-```
-src/
-├── api/          # REST endpoints (auth in auth.js, orders in orders/)
-├── models/       # Sequelize models (User, Product, Order)
-├── services/     # Stripe (payments/), SendGrid (email/)
-├── client/       # React app (components/, pages/, hooks/)
-└── shared/       # Types and constants used by both API and client
-```
-
-## Architecture
-RESTful API with JWT auth. React frontend calls API. Background jobs via Bull queue. PostgreSQL with Sequelize ORM.
-
-## Key Files
-- Entry: `src/index.js` (starts Express server)
-- Config: `src/config/` (env-specific settings)
-- Routes: `src/api/routes.js` (all endpoints defined here)
-- Auth: `src/middleware/auth.js` (JWT validation)
-
-## Conventions
-- Files named `[entity].service.js` handle business logic
-- All API routes return `{ success: boolean, data?: any, error?: string }`
-- Database migrations in `migrations/` - run before adding models
-
-## Important Notes
-- Payment webhooks MUST be idempotent (check `processedWebhooks` table)
-- User emails are case-insensitive (lowercase in DB)
-- Order status transitions enforced in `Order.beforeUpdate` hook
-````""",
+                    description=(
+                        "Creates a concise codebase overview for AI agents. Focus on "
+                        "essential navigation and context in 3500-7000 words. Include: "
+                        "(1) One-paragraph system summary - what it does and its core "
+                        "purpose, (2) Directory tree with one-line descriptions for "
+                        "each major folder, (3) Key architectural patterns (e.g., MVC, "
+                        "microservices, event-driven) in 2-3 sentences, (4) Critical "
+                        "file locations (entry points, config, main business logic), "
+                        "(5) Essential conventions (naming, file organization, error "
+                        "handling), (6) Important gotchas or non-obvious connections. "
+                        "Keep it scannable and action-oriented.\n\n"
+                        "Example:\n\n"
+                        "````\n"
+                        "## System Summary\n"
+                        "E-commerce platform handling product catalog, orders, "
+                        "and payments with React frontend and Node.js API.\n\n"
+                        "## Directory Structure\n"
+                        "```\n"
+                        "src/\n"
+                        "├── api/          # REST endpoints "
+                        "(auth in auth.js, orders in orders/)\n"
+                        "├── models/       # Sequelize models "
+                        "(User, Product, Order)\n"
+                        "├── services/     # Stripe (payments/), "
+                        "SendGrid (email/)\n"
+                        "├── client/       # React app "
+                        "(components/, pages/, hooks/)\n"
+                        "└── shared/       # Types and constants used "
+                        "by both API and client\n"
+                        "```\n\n"
+                        "## Architecture\n"
+                        "RESTful API with JWT auth. React frontend calls API. "
+                        "Background jobs via Bull queue. PostgreSQL with "
+                        "Sequelize ORM.\n\n"
+                        "## Key Files\n"
+                        "- Entry: `src/index.js` "
+                        "(starts Express server)\n"
+                        "- Config: `src/config/` "
+                        "(env-specific settings)\n"
+                        "- Routes: `src/api/routes.js` "
+                        "(all endpoints defined here)\n"
+                        "- Auth: `src/middleware/auth.js` "
+                        "(JWT validation)\n\n"
+                        "## Conventions\n"
+                        "- Files named `[entity].service.js` "
+                        "handle business logic\n"
+                        "- All API routes return "
+                        "`{ success: boolean, data?: any, error?: string }`\n"
+                        "- Database migrations in `migrations/` - "
+                        "run before adding models\n\n"
+                        "## Important Notes\n"
+                        "- Payment webhooks MUST be idempotent "
+                        "(check `processedWebhooks` table)\n"
+                        "- User emails are case-insensitive "
+                        "(lowercase in DB)\n"
+                        "- Order status transitions enforced in "
+                        "`Order.beforeUpdate` hook\n"
+                        "````"
+                    ),
                     inputSchema={
                         "type": "object",
                         "properties": {
-                            "projectName": {"type": "string", "description": "The name of the project"},
-                            "folderPath": {"type": "string", "description": "Absolute path to the project folder on disk"},
-                            "overview": {"type": "string", "description": "Concise codebase overview (aim for 3500-7500 words / 5k-10k tokens)"}
+                            "projectName": {
+                                "type": "string",
+                                "description": "The name of the project",
+                            },
+                            "folderPath": {
+                                "type": "string",
+                                "description": (
+                                    "Absolute path to the project folder on disk"
+                                ),
+                            },
+                            "overview": {
+                                "type": "string",
+                                "description": (
+                                    "Concise codebase overview "
+                                    "(aim for 3500-7500 words / 5k-10k tokens)"
+                                ),
+                            },
                         },
                         "required": ["projectName", "folderPath", "overview"],
-                        "additionalProperties": False
-                    }
+                        "additionalProperties": False,
+                    },
                 ),
                 types.Tool(
                     name="get_word_frequency",
-                    description="Analyzes all file descriptions to find the most frequently used technical terms. Filters out common English stop words and symbols, returning the top 200 meaningful terms. Useful for understanding the codebase's domain vocabulary and finding all functions/files related to specific concepts.",
+                    description=(
+                        "Analyzes all file descriptions to find the most frequently "
+                        "used technical terms. Filters out common English stop words "
+                        "and symbols, returning the top 200 meaningful terms. Useful "
+                        "for understanding the codebase's domain vocabulary and "
+                        "finding all functions/files related to specific concepts."
+                    ),
                     inputSchema={
                         "type": "object",
                         "properties": {
-                            "projectName": {"type": "string", "description": "The name of the project"},
-                            "folderPath": {"type": "string", "description": "Absolute path to the project folder on disk"},
-
-                            "limit": {"type": "integer", "default": 200, "description": "Number of top terms to return"}
+                            "projectName": {
+                                "type": "string",
+                                "description": "The name of the project",
+                            },
+                            "folderPath": {
+                                "type": "string",
+                                "description": (
+                                    "Absolute path to the project folder on disk"
+                                ),
+                            },
+                            "limit": {
+                                "type": "integer",
+                                "default": 200,
+                                "description": "Number of top terms to return",
+                            },
                         },
                         "required": ["projectName", "folderPath"],
-                        "additionalProperties": False
-                    }
+                        "additionalProperties": False,
+                    },
                 ),
                 types.Tool(
                     name="check_database_health",
-                    description="Perform health diagnostics for the MCP Code Indexer's SQLite database and connection pool. Returns database resilience metrics, connection pool status, WAL mode performance, and file description storage statistics for monitoring the code indexer's database locking improvements.",
+                    description=(
+                        "Perform health diagnostics for the MCP Code Indexer's SQLite "
+                        "database and connection pool. Returns database resilience "
+                        "metrics, connection pool status, WAL mode performance, and "
+                        "file description storage statistics for monitoring the code "
+                        "indexer's database locking improvements."
+                    ),
                     inputSchema={
                         "type": "object",
                         "properties": {},
-                        "additionalProperties": False
-                    }
+                        "additionalProperties": False,
+                    },
                 ),
                 types.Tool(
                     name="search_codebase_overview",
-                    description="Search for a single word in the codebase overview and return 2 sentences before and after where the word is found. Useful for quickly finding specific information in large overviews.",
+                    description=(
+                        "Search for a single word in the codebase overview and return "
+                        "2 sentences before and after where the word is found. Useful "
+                        "for quickly finding specific information in large overviews."
+                    ),
                     inputSchema={
                         "type": "object",
                         "properties": {
-                            "projectName": {"type": "string", "description": "The name of the project"},
-                            "folderPath": {"type": "string", "description": "Absolute path to the project folder on disk"},
-
-                            "searchWord": {"type": "string", "description": "Single word to search for in the overview"}
+                            "projectName": {
+                                "type": "string",
+                                "description": "The name of the project",
+                            },
+                            "folderPath": {
+                                "type": "string",
+                                "description": (
+                                    "Absolute path to the project folder on disk"
+                                ),
+                            },
+                            "searchWord": {
+                                "type": "string",
+                                "description": (
+                                    "Single word to search for in the overview"
+                                ),
+                            },
                         },
                         "required": ["projectName", "folderPath", "searchWord"],
-                        "additionalProperties": False
-                    }
-                )
+                        "additionalProperties": False,
+                    },
+                ),
             ]
-        
+
         @self.server.call_tool()
-        async def call_tool(name: str, arguments: Dict[str, Any]) -> List[types.TextContent]:
+        async def call_tool(
+            name: str, arguments: Dict[str, Any]
+        ) -> List[types.TextContent]:
             """Handle tool calls with middleware."""
             import time
+
             start_time = time.time()
-            
+
             logger.info(f"=== MCP Tool Call: {name} ===")
             logger.info(f"Arguments: {', '.join(arguments.keys())}")
-            
+
             # Map tool names to handler methods
             tool_handlers = {
                 "get_file_description": self._handle_get_file_description,
@@ -458,67 +670,69 @@ RESTful API with JWT auth. React frontend calls API. Background jobs via Bull qu
                 "get_codebase_overview": self._handle_get_condensed_overview,
                 "update_codebase_overview": self._handle_update_codebase_overview,
                 "get_word_frequency": self._handle_get_word_frequency,
-
                 "check_database_health": self._handle_check_database_health,
                 "search_codebase_overview": self._handle_search_codebase_overview,
             }
-            
+
             if name not in tool_handlers:
                 logger.error(f"Unknown tool requested: {name}")
                 from ..error_handler import ValidationError
+
                 raise ValidationError(f"Unknown tool: {name}")
-            
+
             # Wrap handler with middleware
             wrapped_handler = self.middleware.wrap_tool_handler(name)(
                 lambda args: self._execute_tool_handler(tool_handlers[name], args)
             )
-            
+
             try:
                 result = await wrapped_handler(arguments)
-                
+
                 elapsed_time = time.time() - start_time
-                logger.info(f"MCP Tool '{name}' completed successfully in {elapsed_time:.2f}s")
-                
+                logger.info(
+                    f"MCP Tool '{name}' completed successfully in {elapsed_time:.2f}s"
+                )
+
                 return result
             except Exception as e:
                 elapsed_time = time.time() - start_time
                 logger.error(f"MCP Tool '{name}' failed after {elapsed_time:.2f}s: {e}")
                 logger.error(f"Exception details: {type(e).__name__}: {str(e)}")
                 raise
-    
-    async def _execute_tool_handler(self, handler, arguments: Dict[str, Any]) -> List[types.TextContent]:
+
+    async def _execute_tool_handler(
+        self, handler, arguments: Dict[str, Any]
+    ) -> List[types.TextContent]:
         """Execute a tool handler and format the result."""
         # Clean HTML entities from all arguments before processing
         cleaned_arguments = self._clean_arguments(arguments)
-        
+
         result = await handler(cleaned_arguments)
-        
-        return [types.TextContent(
-            type="text",
-            text=json.dumps(result, indent=2, default=str)
-        )]
-    
+
+        return [
+            types.TextContent(
+                type="text", text=json.dumps(result, indent=2, default=str)
+            )
+        ]
+
     async def _get_or_create_project_id(self, arguments: Dict[str, Any]) -> str:
         """
         Get or create a project ID using intelligent matching.
-        
+
         Matches projects based on identification factors:
         1. Project name (normalized, case-insensitive)
         2. Folder path in aliases
-        
+
         Projects are now identified primarily by name without git coupling.
         """
         project_name = arguments["projectName"]
         folder_path = arguments["folderPath"]
 
-        
         # Normalize project name for case-insensitive matching
         normalized_name = project_name.lower()
-        
+
         # Find potential project matches
-        project = await self._find_matching_project(
-            normalized_name, folder_path
-        )
+        project = await self._find_matching_project(normalized_name, folder_path)
         if project:
             # Update project metadata and aliases
             await self._update_existing_project(project, normalized_name, folder_path)
@@ -530,63 +744,72 @@ RESTful API with JWT auth. React frontend calls API. Background jobs via Bull qu
                 name=normalized_name,
                 aliases=[folder_path],
                 created=datetime.utcnow(),
-                last_accessed=datetime.utcnow()
+                last_accessed=datetime.utcnow(),
             )
             await self.db_manager.create_project(project)
             logger.info(f"Created new project: {normalized_name} ({project_id})")
-        
+
         return project.id
-    
+
     async def _find_matching_project(
-        self, 
-        normalized_name: str, 
-        folder_path: str
+        self, normalized_name: str, folder_path: str
     ) -> Optional[Project]:
         """
         Find a matching project using name and folder path matching.
-        
+
         Returns the best matching project or None if no sufficient match is found.
         """
         all_projects = await self.db_manager.get_all_projects()
-        
+
         best_match = None
         best_score = 0
-        
+
         for project in all_projects:
             score = 0
             match_factors = []
-            
+
             # Factor 1: Project name match (primary identifier)
             if project.name.lower() == normalized_name:
                 score += 2  # Higher weight for name match
                 match_factors.append("name")
-            
+
             # Factor 2: Folder path in aliases
-            project_aliases = json.loads(project.aliases) if isinstance(project.aliases, str) else project.aliases
+            project_aliases = (
+                json.loads(project.aliases)
+                if isinstance(project.aliases, str)
+                else project.aliases
+            )
             if folder_path in project_aliases:
                 score += 1
                 match_factors.append("folder_path")
-            
+
             # If we have a name match, it's a strong candidate
             if score >= 2:
                 if score > best_score:
                     best_score = score
                     best_match = project
-                    logger.info(f"Match for project {project.name} (score: {score}, factors: {match_factors})")
-            
+                    logger.info(
+                        f"Match for project {project.name} "
+                        f"(score: {score}, factors: {match_factors})"
+                    )
+
             # If only name matches, check file similarity for potential matches
             elif score == 1 and "name" in match_factors:
                 if await self._check_file_similarity(project, folder_path):
-                    logger.info(f"File similarity match for project {project.name} (factor: {match_factors[0]})")
+                    logger.info(
+                        f"File similarity match for project {project.name} "
+                        f"(factor: {match_factors[0]})"
+                    )
                     if score > best_score:
                         best_score = score
                         best_match = project
-        
+
         return best_match
-    
+
     async def _check_file_similarity(self, project: Project, folder_path: str) -> bool:
         """
-        Check if the files in the folder are similar to files already indexed for this project.
+        Check if the files in the folder are similar to files already indexed
+        for this project.
         Returns True if 80%+ of files match.
         """
         try:
@@ -594,163 +817,182 @@ RESTful API with JWT auth. React frontend calls API. Background jobs via Bull qu
             scanner = FileScanner(Path(folder_path))
             if not scanner.is_valid_project_directory():
                 return False
-            
+
             current_files = scanner.scan_directory()
             current_basenames = {f.name for f in current_files}
-            
+
             if not current_basenames:
                 return False
-            
+
             # Get files already indexed for this project
             indexed_files = await self.db_manager.get_all_file_descriptions(project.id)
             indexed_basenames = {Path(fd.file_path).name for fd in indexed_files}
-            
+
             if not indexed_basenames:
                 return False
-            
+
             # Calculate similarity
             intersection = current_basenames & indexed_basenames
             similarity = len(intersection) / len(current_basenames)
-            
-            logger.debug(f"File similarity for {project.name}: {similarity:.2%} ({len(intersection)}/{len(current_basenames)} files match)")
-            
+
+            logger.debug(
+                f"File similarity for {project.name}: {similarity:.2%} "
+                f"({len(intersection)}/{len(current_basenames)} files match)"
+            )
+
             return similarity >= 0.8
         except Exception as e:
             logger.warning(f"Error checking file similarity: {e}")
             return False
-    
+
     async def _update_existing_project(
-        self, 
-        project: Project, 
-        normalized_name: str,
-        folder_path: str
+        self, project: Project, normalized_name: str, folder_path: str
     ) -> None:
         """Update an existing project with new metadata and folder alias."""
         # Update last accessed time
         await self.db_manager.update_project_access_time(project.id)
-        
+
         should_update = False
-        
+
         # Update name if different
         if project.name != normalized_name:
             project.name = normalized_name
             should_update = True
-        
+
         # Add folder path to aliases if not already present
-        project_aliases = json.loads(project.aliases) if isinstance(project.aliases, str) else project.aliases
+        project_aliases = (
+            json.loads(project.aliases)
+            if isinstance(project.aliases, str)
+            else project.aliases
+        )
         if folder_path not in project_aliases:
             project_aliases.append(folder_path)
             project.aliases = project_aliases
             should_update = True
-            logger.info(f"Added new folder alias to project {project.name}: {folder_path}")
-        
+            logger.info(
+                f"Added new folder alias to project {project.name}: {folder_path}"
+            )
+
         if should_update:
             await self.db_manager.update_project(project)
             logger.debug(f"Updated project metadata for {project.name}")
-    
 
-    
-    async def _handle_get_file_description(self, arguments: Dict[str, Any]) -> Dict[str, Any]:
+    async def _handle_get_file_description(
+        self, arguments: Dict[str, Any]
+    ) -> Dict[str, Any]:
         """Handle get_file_description tool calls."""
         project_id = await self._get_or_create_project_id(arguments)
-        
+
         file_desc = await self.db_manager.get_file_description(
-            project_id=project_id,
-            file_path=arguments["filePath"]
+            project_id=project_id, file_path=arguments["filePath"]
         )
-        
+
         if file_desc:
             return {
                 "exists": True,
                 "description": file_desc.description,
                 "lastModified": file_desc.last_modified.isoformat(),
                 "fileHash": file_desc.file_hash,
-                "version": file_desc.version
+                "version": file_desc.version,
             }
         else:
             return {
                 "exists": False,
-                "message": f"No description found for {arguments['filePath']}"
+                "message": f"No description found for {arguments['filePath']}",
             }
-    
-    async def _handle_update_file_description(self, arguments: Dict[str, Any]) -> Dict[str, Any]:
+
+    async def _handle_update_file_description(
+        self, arguments: Dict[str, Any]
+    ) -> Dict[str, Any]:
         """Handle update_file_description tool calls."""
         logger.info(f"Updating file description for: {arguments['filePath']}")
         logger.info(f"Project: {arguments.get('projectName', 'Unknown')}")
-        
+
         description_length = len(arguments.get("description", ""))
         logger.info(f"Description length: {description_length} characters")
-        
+
         project_id = await self._get_or_create_project_id(arguments)
-        
+
         logger.info(f"Resolved project_id: {project_id}")
-        
+
         file_desc = FileDescription(
             project_id=project_id,
             file_path=arguments["filePath"],
             description=arguments["description"],
             file_hash=arguments.get("fileHash"),
             last_modified=datetime.utcnow(),
-            version=1
+            version=1,
         )
-        
+
         await self.db_manager.create_file_description(file_desc)
-        
+
         logger.info(f"Successfully updated description for: {arguments['filePath']}")
-        
+
         return {
             "success": True,
             "message": f"Description updated for {arguments['filePath']}",
             "filePath": arguments["filePath"],
-            "lastModified": file_desc.last_modified.isoformat()
+            "lastModified": file_desc.last_modified.isoformat(),
         }
-    
-    async def _handle_check_codebase_size(self, arguments: Dict[str, Any]) -> Dict[str, Any]:
+
+    async def _handle_check_codebase_size(
+        self, arguments: Dict[str, Any]
+    ) -> Dict[str, Any]:
         """Handle check_codebase_size tool calls."""
-        logger.info(f"Checking codebase size for: {arguments.get('projectName', 'Unknown')}")
+        logger.info(
+            f"Checking codebase size for: {arguments.get('projectName', 'Unknown')}"
+        )
         logger.info(f"Folder path: {arguments.get('folderPath', 'Unknown')}")
-        
+
         project_id = await self._get_or_create_project_id(arguments)
         folder_path = Path(arguments["folderPath"])
-        
+
         logger.info(f"Resolved project_id: {project_id}")
-        
+
         # Clean up descriptions for files that no longer exist
         logger.info("Cleaning up descriptions for missing files...")
         cleaned_up_files = await self.db_manager.cleanup_missing_files(
-            project_id=project_id,
-            project_root=folder_path
+            project_id=project_id, project_root=folder_path
         )
         logger.info(f"Cleaned up {len(cleaned_up_files)} missing files")
-        
+
         # Get file descriptions for this project (after cleanup)
         logger.info("Retrieving file descriptions...")
         file_descriptions = await self.db_manager.get_all_file_descriptions(
             project_id=project_id
         )
         logger.info(f"Found {len(file_descriptions)} file descriptions")
-        
+
         # Use provided token limit or fall back to server default
         token_limit = arguments.get("tokenLimit", self.token_limit)
-        
+
         # Calculate total tokens for descriptions
         logger.info("Calculating total token count...")
-        descriptions_tokens = self.token_counter.calculate_codebase_tokens(file_descriptions)
-        
+        descriptions_tokens = self.token_counter.calculate_codebase_tokens(
+            file_descriptions
+        )
+
         # Get overview tokens if available
         overview = await self.db_manager.get_project_overview(project_id)
         overview_tokens = 0
         if overview and overview.overview:
             overview_tokens = self.token_counter.count_tokens(overview.overview)
-        
+
         total_tokens = descriptions_tokens + overview_tokens
         is_large = total_tokens > token_limit
         recommendation = "use_search" if is_large else "use_overview"
-        
-        logger.info(f"Codebase analysis complete: {total_tokens} tokens total ({descriptions_tokens} descriptions + {overview_tokens} overview), {len(file_descriptions)} files")
-        logger.info(f"Size assessment: {'LARGE' if is_large else 'SMALL'} (limit: {token_limit})")
+
+        logger.info(
+            f"Codebase analysis complete: {total_tokens} tokens total "
+            f"({descriptions_tokens} descriptions + {overview_tokens} overview), "
+            f"{len(file_descriptions)} files"
+        )
+        logger.info(
+            f"Size assessment: {'LARGE' if is_large else 'SMALL'} "
+            f"(limit: {token_limit})"
+        )
         logger.info(f"Recommendation: {recommendation}")
-        
+
         return {
             "totalTokens": total_tokens,
             "descriptionsTokens": descriptions_tokens,
@@ -760,19 +1002,24 @@ RESTful API with JWT auth. React frontend calls API. Background jobs via Bull qu
             "tokenLimit": token_limit,
             "totalFiles": len(file_descriptions),
             "cleanedUpFiles": cleaned_up_files,
-            "cleanedUpCount": len(cleaned_up_files)
+            "cleanedUpCount": len(cleaned_up_files),
         }
-    
-    async def _handle_find_missing_descriptions(self, arguments: Dict[str, Any]) -> Dict[str, Any]:
+
+    async def _handle_find_missing_descriptions(
+        self, arguments: Dict[str, Any]
+    ) -> Dict[str, Any]:
         """Handle find_missing_descriptions tool calls."""
-        logger.info(f"Finding missing descriptions for: {arguments.get('projectName', 'Unknown')}")
+        logger.info(
+            f"Finding missing descriptions for: "
+            f"{arguments.get('projectName', 'Unknown')}"
+        )
         logger.info(f"Folder path: {arguments.get('folderPath', 'Unknown')}")
-        
+
         project_id = await self._get_or_create_project_id(arguments)
         folder_path = Path(arguments["folderPath"])
-        
+
         logger.info(f"Resolved project_id: {project_id}")
-        
+
         # Get existing file descriptions
         logger.info("Retrieving existing file descriptions...")
         existing_descriptions = await self.db_manager.get_all_file_descriptions(
@@ -780,7 +1027,7 @@ RESTful API with JWT auth. React frontend calls API. Background jobs via Bull qu
         )
         existing_paths = {desc.file_path for desc in existing_descriptions}
         logger.info(f"Found {len(existing_paths)} existing descriptions")
-        
+
         # Scan directory for files
         logger.info(f"Scanning project directory: {folder_path}")
         scanner = FileScanner(folder_path)
@@ -789,110 +1036,116 @@ RESTful API with JWT auth. React frontend calls API. Background jobs via Bull qu
             return {
                 "error": f"Invalid or inaccessible project directory: {folder_path}"
             }
-        
+
         missing_files = scanner.find_missing_files(existing_paths)
         missing_paths = [scanner.get_relative_path(f) for f in missing_files]
-        
+
         logger.info(f"Found {len(missing_paths)} files without descriptions")
-        
+
         # Apply limit if specified
         limit = arguments.get("limit")
         total_missing = len(missing_paths)
         if limit is not None and isinstance(limit, int) and limit > 0:
             missing_paths = missing_paths[:limit]
             logger.info(f"Applied limit {limit}, returning {len(missing_paths)} files")
-        
+
         # Get project stats
         stats = scanner.get_project_stats()
         logger.info(f"Project stats: {stats.get('total_files', 0)} total files")
-        
+
         return {
             "missingFiles": missing_paths,
             "totalMissing": total_missing,
             "returnedCount": len(missing_paths),
             "existingDescriptions": len(existing_paths),
-            "projectStats": stats
+            "projectStats": stats,
         }
-    
-    async def _handle_search_descriptions(self, arguments: Dict[str, Any]) -> Dict[str, Any]:
+
+    async def _handle_search_descriptions(
+        self, arguments: Dict[str, Any]
+    ) -> Dict[str, Any]:
         """Handle search_descriptions tool calls."""
         project_id = await self._get_or_create_project_id(arguments)
         max_results = arguments.get("maxResults", 20)
-        
+
         # Perform search
         search_results = await self.db_manager.search_file_descriptions(
-            project_id=project_id,
-            query=arguments["query"],
-            max_results=max_results
+            project_id=project_id, query=arguments["query"], max_results=max_results
         )
-        
+
         # Format results
         formatted_results = []
         for result in search_results:
-            formatted_results.append({
-                "filePath": result.file_path,
-                "description": result.description,
-                "relevanceScore": result.relevance_score
-            })
-        
+            formatted_results.append(
+                {
+                    "filePath": result.file_path,
+                    "description": result.description,
+                    "relevanceScore": result.relevance_score,
+                }
+            )
+
         return {
             "results": formatted_results,
             "totalResults": len(formatted_results),
             "query": arguments["query"],
-            "maxResults": max_results
+            "maxResults": max_results,
         }
-    
-    async def _handle_get_codebase_overview(self, arguments: Dict[str, Any]) -> Dict[str, Any]:
+
+    async def _handle_get_codebase_overview(
+        self, arguments: Dict[str, Any]
+    ) -> Dict[str, Any]:
         """Handle get_codebase_overview tool calls."""
         project_id = await self._get_or_create_project_id(arguments)
-        
+
         # Get all file descriptions
         file_descriptions = await self.db_manager.get_all_file_descriptions(
             project_id=project_id
         )
-        
+
         # Calculate total tokens
         total_tokens = self.token_counter.calculate_codebase_tokens(file_descriptions)
         is_large = self.token_counter.is_large_codebase(total_tokens)
-        
-        # Always build and return the folder structure - if the AI called this tool, it wants the overview
+
+        # Always build and return the folder structure - if the AI called this
+        # tool, it wants the overview
         structure = self._build_folder_structure(file_descriptions)
-        
+
         return {
             "projectName": arguments["projectName"],
             "totalFiles": len(file_descriptions),
             "totalTokens": total_tokens,
             "isLarge": is_large,
             "tokenLimit": self.token_counter.token_limit,
-            "structure": structure
+            "structure": structure,
         }
-    
-    def _build_folder_structure(self, file_descriptions: List[FileDescription]) -> Dict[str, Any]:
+
+    def _build_folder_structure(
+        self, file_descriptions: List[FileDescription]
+    ) -> Dict[str, Any]:
         """Build hierarchical folder structure from file descriptions."""
         root = {"path": "", "files": [], "folders": {}}
-        
+
         for file_desc in file_descriptions:
             path_parts = Path(file_desc.file_path).parts
             current = root
-            
+
             # Navigate/create folder structure
             for i, part in enumerate(path_parts[:-1]):
-                folder_path = "/".join(path_parts[:i+1])
+                folder_path = "/".join(path_parts[: i + 1])
                 if part not in current["folders"]:
                     current["folders"][part] = {
                         "path": folder_path,
                         "files": [],
-                        "folders": {}
+                        "folders": {},
                     }
                 current = current["folders"][part]
-            
+
             # Add file to current folder
             if path_parts:  # Handle empty paths
-                current["files"].append({
-                    "path": file_desc.file_path,
-                    "description": file_desc.description
-                })
-        
+                current["files"].append(
+                    {"path": file_desc.file_path, "description": file_desc.description}
+                )
+
         # Convert nested dict structure to list format, skipping empty folders
         def convert_structure(node):
             folders = []
@@ -901,108 +1154,112 @@ RESTful API with JWT auth. React frontend calls API. Background jobs via Bull qu
                 # Only include folders that have files or non-empty subfolders
                 if converted_folder["files"] or converted_folder["folders"]:
                     folders.append(converted_folder)
-            
-            return {
-                "path": node["path"],
-                "files": node["files"],
-                "folders": folders
-            }
-        
+
+            return {"path": node["path"], "files": node["files"], "folders": folders}
+
         return convert_structure(root)
-    
 
-    
-    async def _handle_get_condensed_overview(self, arguments: Dict[str, Any]) -> Dict[str, Any]:
+    async def _handle_get_condensed_overview(
+        self, arguments: Dict[str, Any]
+    ) -> Dict[str, Any]:
         """Handle get_codebase_overview tool calls for condensed overviews."""
         project_id = await self._get_or_create_project_id(arguments)
-        
+
         # Try to get existing overview
         overview = await self.db_manager.get_project_overview(project_id)
-        
+
         if overview:
             return {
                 "overview": overview.overview,
                 "lastModified": overview.last_modified.isoformat(),
                 "totalFiles": overview.total_files,
-                "totalTokensInFullDescriptions": overview.total_tokens
+                "totalTokensInFullDescriptions": overview.total_tokens,
             }
         else:
             return {
                 "overview": "",
                 "lastModified": "",
                 "totalFiles": 0,
-                "totalTokensInFullDescriptions": 0
+                "totalTokensInFullDescriptions": 0,
             }
-    
-    async def _handle_update_codebase_overview(self, arguments: Dict[str, Any]) -> Dict[str, Any]:
+
+    async def _handle_update_codebase_overview(
+        self, arguments: Dict[str, Any]
+    ) -> Dict[str, Any]:
         """Handle update_codebase_overview tool calls."""
         project_id = await self._get_or_create_project_id(arguments)
-        folder_path = Path(arguments["folderPath"])
-        
+
         # Get current file count and total tokens for context
         file_descriptions = await self.db_manager.get_all_file_descriptions(
             project_id=project_id
         )
-        
+
         total_files = len(file_descriptions)
         total_tokens = self.token_counter.calculate_codebase_tokens(file_descriptions)
-        
+
         # Create overview record
         overview = ProjectOverview(
             project_id=project_id,
             overview=arguments["overview"],
             last_modified=datetime.utcnow(),
             total_files=total_files,
-            total_tokens=total_tokens
+            total_tokens=total_tokens,
         )
-        
+
         await self.db_manager.create_project_overview(overview)
-        
+
         return {
             "success": True,
             "message": f"Overview updated for {total_files} files",
             "totalFiles": total_files,
             "totalTokens": total_tokens,
-            "overviewLength": len(arguments["overview"])
+            "overviewLength": len(arguments["overview"]),
         }
-    
-    async def _handle_get_word_frequency(self, arguments: Dict[str, Any]) -> Dict[str, Any]:
+
+    async def _handle_get_word_frequency(
+        self, arguments: Dict[str, Any]
+    ) -> Dict[str, Any]:
         """Handle get_word_frequency tool calls."""
         project_id = await self._get_or_create_project_id(arguments)
         limit = arguments.get("limit", 200)
-        
+
         # Analyze word frequency
         result = await self.db_manager.analyze_word_frequency(
-            project_id=project_id,
-            limit=limit
+            project_id=project_id, limit=limit
         )
-        
+
         return {
-            "topTerms": [{"term": term.term, "frequency": term.frequency} for term in result.top_terms],
+            "topTerms": [
+                {"term": term.term, "frequency": term.frequency}
+                for term in result.top_terms
+            ],
             "totalTermsAnalyzed": result.total_terms_analyzed,
-            "totalUniqueTerms": result.total_unique_terms
+            "totalUniqueTerms": result.total_unique_terms,
         }
-    
-    async def _handle_search_codebase_overview(self, arguments: Dict[str, Any]) -> Dict[str, Any]:
+
+    async def _handle_search_codebase_overview(
+        self, arguments: Dict[str, Any]
+    ) -> Dict[str, Any]:
         """Handle search_codebase_overview tool calls."""
         project_id = await self._get_or_create_project_id(arguments)
         search_word = arguments["searchWord"].lower()
-        
+
         # Get the overview
         overview = await self.db_manager.get_project_overview(project_id)
-        
+
         if not overview or not overview.overview:
             return {
                 "found": False,
                 "message": "No overview found for this project",
-                "searchWord": arguments["searchWord"]
+                "searchWord": arguments["searchWord"],
             }
-        
+
         # Split overview into sentences
         import re
-        sentences = re.split(r'[.!?]+', overview.overview)
+
+        sentences = re.split(r"[.!?]+", overview.overview)
         sentences = [s.strip() for s in sentences if s.strip()]
-        
+
         # Find matches
         matches = []
         for i, sentence in enumerate(sentences):
@@ -1010,170 +1267,209 @@ RESTful API with JWT auth. React frontend calls API. Background jobs via Bull qu
                 # Get context: 2 sentences before and after
                 start_idx = max(0, i - 2)
                 end_idx = min(len(sentences), i + 3)
-                
+
                 context_sentences = sentences[start_idx:end_idx]
-                context = '. '.join(context_sentences) + '.'
-                
-                matches.append({
-                    "matchIndex": i,
-                    "matchSentence": sentence,
-                    "context": context,
-                    "contextStartIndex": start_idx,
-                    "contextEndIndex": end_idx - 1
-                })
-        
+                context = ". ".join(context_sentences) + "."
+
+                matches.append(
+                    {
+                        "matchIndex": i,
+                        "matchSentence": sentence,
+                        "context": context,
+                        "contextStartIndex": start_idx,
+                        "contextEndIndex": end_idx - 1,
+                    }
+                )
+
         return {
             "found": len(matches) > 0,
             "searchWord": arguments["searchWord"],
             "matches": matches,
             "totalMatches": len(matches),
-            "totalSentences": len(sentences)
+            "totalSentences": len(sentences),
         }
 
-    async def _handle_check_database_health(self, arguments: Dict[str, Any]) -> Dict[str, Any]:
+    async def _handle_check_database_health(
+        self, arguments: Dict[str, Any]
+    ) -> Dict[str, Any]:
         """
         Handle check_database_health tool calls with comprehensive diagnostics.
-        
+
         Returns detailed database health information including retry statistics,
         performance analysis, and resilience indicators.
         """
         # Get comprehensive health diagnostics from the enhanced monitor
-        if hasattr(self.db_manager, '_health_monitor') and self.db_manager._health_monitor:
-            comprehensive_diagnostics = self.db_manager._health_monitor.get_comprehensive_diagnostics()
+        if (
+            hasattr(self.db_manager, "_health_monitor")
+            and self.db_manager._health_monitor
+        ):
+            comprehensive_diagnostics = (
+                self.db_manager._health_monitor.get_comprehensive_diagnostics()
+            )
         else:
             # Fallback to basic health check if monitor not available
             health_check = await self.db_manager.check_health()
             comprehensive_diagnostics = {
                 "basic_health_check": health_check,
-                "note": "Enhanced health monitoring not available"
+                "note": "Enhanced health monitoring not available",
             }
-        
+
         # Get additional database-level statistics
         database_stats = self.db_manager.get_database_stats()
-        
+
         return {
             "comprehensive_diagnostics": comprehensive_diagnostics,
             "database_statistics": database_stats,
             "configuration": {
                 **self.db_config,
                 "retry_executor_config": (
-                    self.db_manager._retry_executor.config.__dict__ 
-                    if hasattr(self.db_manager, '_retry_executor') and self.db_manager._retry_executor 
+                    self.db_manager._retry_executor.config.__dict__
+                    if hasattr(self.db_manager, "_retry_executor")
+                    and self.db_manager._retry_executor
                     else {}
-                )
+                ),
             },
             "server_info": {
                 "token_limit": self.token_limit,
                 "db_path": str(self.db_path),
                 "cache_dir": str(self.cache_dir),
                 "health_monitoring_enabled": (
-                    hasattr(self.db_manager, '_health_monitor') and 
-                    self.db_manager._health_monitor is not None
-                )
+                    hasattr(self.db_manager, "_health_monitor")
+                    and self.db_manager._health_monitor is not None
+                ),
             },
             "timestamp": datetime.utcnow().isoformat(),
-            "status_summary": self._generate_health_summary(comprehensive_diagnostics)
+            "status_summary": self._generate_health_summary(comprehensive_diagnostics),
         }
-    
+
     def _generate_health_summary(self, diagnostics: Dict[str, Any]) -> Dict[str, Any]:
         """Generate a concise health summary from comprehensive diagnostics."""
         if "resilience_indicators" not in diagnostics:
             return {"status": "limited_diagnostics_available"}
-        
+
         resilience = diagnostics["resilience_indicators"]
         performance = diagnostics.get("performance_analysis", {})
-        
+
         # Overall status based on health score
         health_score = resilience.get("overall_health_score", 0)
         if health_score >= 90:
             status = "excellent"
         elif health_score >= 75:
-            status = "good"  
+            status = "good"
         elif health_score >= 50:
             status = "fair"
         else:
             status = "poor"
-        
+
         return {
             "overall_status": status,
             "health_score": health_score,
-            "retry_effectiveness": resilience.get("retry_effectiveness", {}).get("is_effective", False),
-            "connection_stability": resilience.get("connection_stability", {}).get("is_stable", False),
-            "key_recommendations": resilience.get("recommendations", [])[:3],  # Top 3 recommendations
-            "performance_trend": performance.get("health_check_performance", {}).get("recent_performance_trend", "unknown")
+            "retry_effectiveness": resilience.get("retry_effectiveness", {}).get(
+                "is_effective", False
+            ),
+            "connection_stability": resilience.get("connection_stability", {}).get(
+                "is_stable", False
+            ),
+            "key_recommendations": resilience.get("recommendations", [])[
+                :3
+            ],  # Top 3 recommendations
+            "performance_trend": performance.get("health_check_performance", {}).get(
+                "recent_performance_trend", "unknown"
+            ),
         }
-    
-    async def _run_session_with_retry(self, read_stream, write_stream, initialization_options) -> None:
+
+    async def _run_session_with_retry(
+        self, read_stream, write_stream, initialization_options
+    ) -> None:
         """Run a single MCP session with error handling and retry logic."""
         max_retries = 3
         base_delay = 1.0  # seconds
-        
+
         for attempt in range(max_retries + 1):
             try:
-                logger.info(f"Starting MCP server protocol session (attempt {attempt + 1})...")
-                await self.server.run(
-                    read_stream,
-                    write_stream, 
-                    initialization_options
+                logger.info(
+                    f"Starting MCP server protocol session (attempt {attempt + 1})..."
                 )
+                await self.server.run(read_stream, write_stream, initialization_options)
                 logger.info("MCP server session completed normally")
                 return  # Success, exit retry loop
-                
+
             except ValidationError as e:
                 # Handle malformed requests gracefully
-                logger.warning(f"Received malformed request (attempt {attempt + 1}): {e}", extra={
-                    "structured_data": {
-                        "error_type": "ValidationError",
-                        "validation_errors": e.errors() if hasattr(e, 'errors') else str(e),
-                        "attempt": attempt + 1,
-                        "max_retries": max_retries
-                    }
-                })
-                
+                logger.warning(
+                    f"Received malformed request (attempt {attempt + 1}): {e}",
+                    extra={
+                        "structured_data": {
+                            "error_type": "ValidationError",
+                            "validation_errors": (
+                                e.errors() if hasattr(e, "errors") else str(e)
+                            ),
+                            "attempt": attempt + 1,
+                            "max_retries": max_retries,
+                        }
+                    },
+                )
+
                 if attempt < max_retries:
-                    delay = base_delay * (2 ** attempt)  # Exponential backoff
+                    delay = base_delay * (2**attempt)  # Exponential backoff
                     logger.info(f"Retrying in {delay} seconds...")
                     await asyncio.sleep(delay)
                 else:
-                    logger.error("Max retries exceeded for validation errors. Server will continue but this session failed.")
+                    logger.error(
+                        "Max retries exceeded for validation errors. Server will "
+                        "continue but this session failed."
+                    )
                     return
-                    
+
             except (ConnectionError, BrokenPipeError, EOFError) as e:
                 # Handle client disconnection gracefully
                 logger.info(f"Client disconnected: {e}")
                 return
-                
+
             except Exception as e:
                 # Handle other exceptions with full logging
                 import traceback
-                if "unhandled errors in a TaskGroup" in str(e) and "ValidationError" in str(e):
+
+                if "unhandled errors in a TaskGroup" in str(
+                    e
+                ) and "ValidationError" in str(e):
                     # This is likely a ValidationError wrapped in a TaskGroup exception
-                    logger.warning(f"Detected wrapped validation error (attempt {attempt + 1}): {e}", extra={
-                        "structured_data": {
-                            "error_type": type(e).__name__, 
-                            "error_message": str(e),
-                            "attempt": attempt + 1,
-                            "max_retries": max_retries,
-                            "likely_validation_error": True
-                        }
-                    })
-                    
+                    logger.warning(
+                        f"Detected wrapped validation error "
+                        f"(attempt {attempt + 1}): {e}",
+                        extra={
+                            "structured_data": {
+                                "error_type": type(e).__name__,
+                                "error_message": str(e),
+                                "attempt": attempt + 1,
+                                "max_retries": max_retries,
+                                "likely_validation_error": True,
+                            }
+                        },
+                    )
+
                     if attempt < max_retries:
-                        delay = base_delay * (2 ** attempt)
+                        delay = base_delay * (2**attempt)
                         logger.info(f"Retrying in {delay} seconds...")
                         await asyncio.sleep(delay)
                     else:
-                        logger.error("Max retries exceeded for validation errors. Server will continue but this session failed.")
+                        logger.error(
+                            "Max retries exceeded for validation errors. Server will "
+                            "continue but this session failed."
+                        )
                         return
                 else:
                     # This is a genuine error, log and re-raise
-                    logger.error(f"MCP server session error: {e}", extra={
-                        "structured_data": {
-                            "error_type": type(e).__name__, 
-                            "error_message": str(e),
-                            "traceback": traceback.format_exc()
-                        }
-                    })
+                    logger.error(
+                        f"MCP server session error: {e}",
+                        extra={
+                            "structured_data": {
+                                "error_type": type(e).__name__,
+                                "error_message": str(e),
+                                "traceback": traceback.format_exc(),
+                            }
+                        },
+                    )
                     raise
 
     async def run(self) -> None:
@@ -1181,80 +1477,99 @@ RESTful API with JWT auth. React frontend calls API. Background jobs via Bull qu
         logger.info("Starting server initialization...")
         await self.initialize()
         logger.info("Server initialization completed, starting MCP protocol...")
-        
+
         max_retries = 5
         base_delay = 2.0  # seconds
-        
+
         for attempt in range(max_retries + 1):
             try:
                 async with stdio_server() as (read_stream, write_stream):
-                    logger.info(f"stdio_server context established (attempt {attempt + 1})")
+                    logger.info(
+                        f"stdio_server context established (attempt {attempt + 1})"
+                    )
                     initialization_options = self.server.create_initialization_options()
                     logger.debug(f"Initialization options: {initialization_options}")
-                    
-                    await self._run_session_with_retry(read_stream, write_stream, initialization_options)
+
+                    await self._run_session_with_retry(
+                        read_stream, write_stream, initialization_options
+                    )
                     return  # Success, exit retry loop
-                        
+
             except KeyboardInterrupt:
                 logger.info("Server stopped by user interrupt")
                 return
-                
+
             except Exception as e:
                 import traceback
-                
+
                 # Check if this is a wrapped validation error
                 error_str = str(e)
                 is_validation_error = (
-                    "ValidationError" in error_str or 
-                    "Field required" in error_str or 
-                    "Input should be" in error_str or
-                    "pydantic_core._pydantic_core.ValidationError" in error_str
+                    "ValidationError" in error_str
+                    or "Field required" in error_str
+                    or "Input should be" in error_str
+                    or "pydantic_core._pydantic_core.ValidationError" in error_str
                 )
-                
+
                 if is_validation_error:
-                    logger.warning(f"Detected validation error in session (attempt {attempt + 1}): Malformed client request", extra={
-                        "structured_data": {
-                            "error_type": "ValidationError", 
-                            "error_message": "Client sent malformed request (likely missing clientInfo)",
-                            "attempt": attempt + 1,
-                            "max_retries": max_retries,
-                            "will_retry": attempt < max_retries
-                        }
-                    })
-                    
+                    logger.warning(
+                        f"Detected validation error in session "
+                        f"(attempt {attempt + 1}): Malformed client request",
+                        extra={
+                            "structured_data": {
+                                "error_type": "ValidationError",
+                                "error_message": (
+                                    "Client sent malformed request "
+                                    "(likely missing clientInfo)"
+                                ),
+                                "attempt": attempt + 1,
+                                "max_retries": max_retries,
+                                "will_retry": attempt < max_retries,
+                            }
+                        },
+                    )
+
                     if attempt < max_retries:
-                        delay = base_delay * (2 ** min(attempt, 3))  # Cap exponential growth
+                        delay = base_delay * (
+                            2 ** min(attempt, 3)
+                        )  # Cap exponential growth
                         logger.info(f"Retrying server in {delay} seconds...")
                         await asyncio.sleep(delay)
                         continue
                     else:
-                        logger.warning("Max retries exceeded for validation errors. Server is robust against malformed requests.")
+                        logger.warning(
+                            "Max retries exceeded for validation errors. Server is "
+                            "robust against malformed requests."
+                        )
                         return
                 else:
                     # This is a genuine fatal error
-                    logger.error(f"Fatal server error: {e}", extra={
-                        "structured_data": {
-                            "error_type": type(e).__name__, 
-                            "error_message": str(e),
-                            "traceback": traceback.format_exc()
-                        }
-                    })
+                    logger.error(
+                        f"Fatal server error: {e}",
+                        extra={
+                            "structured_data": {
+                                "error_type": type(e).__name__,
+                                "error_message": str(e),
+                                "traceback": traceback.format_exc(),
+                            }
+                        },
+                    )
                     raise
-        
+
         # Clean shutdown
         await self.shutdown()
-    
+
     async def shutdown(self) -> None:
         """Clean shutdown of server resources."""
         try:
             # Cancel any running tasks
             self.task_manager.cancel_all()
-            
+
             # Close database connections
             await self.db_manager.close_pool()
-            
+
             self.logger.info("Server shutdown completed successfully")
-            
+
         except Exception as e:
             self.error_handler.log_error(e, context={"phase": "shutdown"})
 
@@ -1262,14 +1577,14 @@ RESTful API with JWT auth. React frontend calls API. Background jobs via Bull qu
 async def main():
     """Main entry point for the MCP server."""
     import sys
-    
+
     # Setup logging to stderr (stdout is used for MCP communication)
     logging.basicConfig(
         level=logging.INFO,
         format="%(asctime)s - %(name)s - %(levelname)s - %(message)s",
-        handlers=[logging.StreamHandler(sys.stderr)]
+        handlers=[logging.StreamHandler(sys.stderr)],
     )
-    
+
     # Create and run server
     server = MCPCodeIndexServer()
     await server.run()