mcp-code-indexer 3.1.3__py3-none-any.whl → 3.1.5__py3-none-any.whl

mcp_code_indexer/main.py

@@ -8,10 +8,8 @@ Entry point for the mcp-code-indexer package when installed via pip.
 import argparse
 import asyncio
 import json
-import logging
 import sys
 from pathlib import Path
-from typing import Any, Dict
 
 from . import __version__
 from .logging_config import setup_logging
@@ -22,86 +20,96 @@ def parse_arguments() -> argparse.Namespace:
     """Parse command line arguments."""
     parser = argparse.ArgumentParser(
         description="MCP Code Index Server - Track file descriptions across codebases",
-        prog="mcp-code-indexer"
+        prog="mcp-code-indexer",
     )
-    
+
     parser.add_argument(
-        "--version",
-        action="version",
-        version=f"mcp-code-indexer {__version__}"
+        "--version", action="version", version=f"mcp-code-indexer {__version__}"
     )
-    
+
     parser.add_argument(
         "--token-limit",
         type=int,
         default=32000,
-        help="Maximum tokens before recommending search instead of full overview (default: 32000)"
+        help=(
+            "Maximum tokens before recommending search instead of full overview "
+            "(default: 32000)"
+        ),
     )
-    
+
     parser.add_argument(
         "--db-path",
         type=str,
         default="~/.mcp-code-index/tracker.db",
-        help="Path to SQLite database (default: ~/.mcp-code-index/tracker.db)"
+        help="Path to SQLite database (default: ~/.mcp-code-index/tracker.db)",
     )
-    
+
     parser.add_argument(
         "--cache-dir",
         type=str,
         default="~/.mcp-code-index/cache",
-        help="Directory for caching token counts (default: ~/.mcp-code-index/cache)"
+        help="Directory for caching token counts (default: ~/.mcp-code-index/cache)",
     )
-    
+
     parser.add_argument(
         "--log-level",
         type=str,
         choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],
         default="INFO",
-        help="Logging level (default: INFO)"
+        help="Logging level (default: INFO)",
     )
-    
+
     # Utility commands
     parser.add_argument(
         "--getprojects",
         action="store_true",
-        help="List all projects with IDs, branches, and description counts"
+        help="List all projects with IDs, branches, and description counts",
     )
-    
+
     parser.add_argument(
         "--runcommand",
         type=str,
-        help="Execute a command using JSON in MCP format (single or multi-line)"
+        help="Execute a command using JSON in MCP format (single or multi-line)",
     )
-    
+
     parser.add_argument(
         "--dumpdescriptions",
         nargs="+",
         metavar=("PROJECT_ID", "BRANCH"),
-        help="Export descriptions for a project. Usage: --dumpdescriptions PROJECT_ID [BRANCH]"
+        help=(
+            "Export descriptions for a project. Usage: "
+            "--dumpdescriptions PROJECT_ID [BRANCH]"
+        ),
     )
-    
+
     parser.add_argument(
         "--githook",
         nargs="*",
         metavar="COMMIT_HASH",
-        help="Git hook mode: auto-update descriptions based on git diff using OpenRouter API. "
-             "Usage: --githook (current changes), --githook HASH (specific commit), "
-             "--githook HASH1 HASH2 (commit range from HASH1 to HASH2)"
+        help=(
+            "Git hook mode: auto-update descriptions based on git diff using "
+            "OpenRouter API. Usage: --githook (current changes), --githook HASH "
+            "(specific commit), --githook HASH1 HASH2 (commit range from "
+            "HASH1 to HASH2)"
+        ),
     )
-    
+
     parser.add_argument(
         "--cleanup",
         action="store_true",
-        help="Remove empty projects (no descriptions and no project overview)"
+        help="Remove empty projects (no descriptions and no project overview)",
     )
-    
+
     parser.add_argument(
         "--map",
         type=str,
         metavar="PROJECT_NAME_OR_ID",
-        help="Generate a markdown project map for the specified project (by name or ID)"
+        help=(
+            "Generate a markdown project map for the specified project "
+            "(by name or ID)"
+        ),
     )
-    
+
     return parser.parse_args()
 
 
@@ -110,26 +118,26 @@ async def handle_getprojects(args: argparse.Namespace) -> None:
     db_manager = None
     try:
         from .database.database import DatabaseManager
-        
+
         # Initialize database
         db_path = Path(args.db_path).expanduser()
         db_manager = DatabaseManager(db_path)
         await db_manager.initialize()
-        
+
         # Get all projects
         projects = await db_manager.get_all_projects()
-        
+
         if not projects:
             print("No projects found.")
             return
-        
+
         print("Projects:")
         print("-" * 80)
-        
+
         for project in projects:
             print(f"ID: {project.id}")
             print(f"Name: {project.name}")
-            
+
             # Get branch information
             try:
                 branch_counts = await db_manager.get_branch_file_counts(project.id)
@@ -141,9 +149,9 @@ async def handle_getprojects(args: argparse.Namespace) -> None:
                     print("Branches: No descriptions found")
             except Exception as e:
                 print(f"Branches: Error loading branch info - {e}")
-            
+
             print("-" * 80)
-    
+
     except Exception as e:
         print(f"Error: {e}", file=sys.stderr)
         sys.exit(1)
@@ -157,103 +165,122 @@ async def handle_runcommand(args: argparse.Namespace) -> None:
     """Handle --runcommand command."""
     from .server.mcp_server import MCPCodeIndexServer
     from .logging_config import setup_command_logger
-    
+
     # Set up dedicated logging for runcommand
     cache_dir = Path(args.cache_dir).expanduser()
     logger = setup_command_logger("runcommand", cache_dir)
-    
-    logger.info("Starting runcommand execution", extra={
-        "structured_data": {
-            "command": args.runcommand,
-            "args": {
-                "token_limit": args.token_limit,
-                "db_path": str(args.db_path),
-                "cache_dir": str(args.cache_dir)
+
+    logger.info(
+        "Starting runcommand execution",
+        extra={
+            "structured_data": {
+                "command": args.runcommand,
+                "args": {
+                    "token_limit": args.token_limit,
+                    "db_path": str(args.db_path),
+                    "cache_dir": str(args.cache_dir),
+                },
             }
-        }
-    })
-    
+        },
+    )
+
     try:
         # Parse JSON (handle both single-line and multi-line)
         logger.debug("Parsing JSON command")
         json_data = json.loads(args.runcommand)
-        logger.debug("JSON parsed successfully", extra={"structured_data": {"parsed_json": json_data}})
+        logger.debug(
+            "JSON parsed successfully",
+            extra={"structured_data": {"parsed_json": json_data}},
+        )
     except json.JSONDecodeError as e:
-        logger.warning("Initial JSON parse failed", extra={"structured_data": {"error": str(e)}})
+        logger.warning(
+            "Initial JSON parse failed", extra={"structured_data": {"error": str(e)}}
+        )
         print(f"Initial JSON parse failed: {e}", file=sys.stderr)
-        
+
         # Try to repair the JSON
         logger.debug("Attempting JSON repair")
         try:
             import re
+
             repaired = args.runcommand
-            
+
             # Fix common issues
             # Quote unquoted URLs and paths
             url_pattern = r'("[\w]+"):\s*([a-zA-Z][a-zA-Z0-9+.-]*://[^\s,}]+|/[^\s,}]*)'
             repaired = re.sub(url_pattern, r'\1: "\2"', repaired)
-            
+
             # Quote unquoted values
             unquoted_pattern = r'("[\w]+"):\s*([a-zA-Z0-9_-]+)(?=\s*[,}])'
             repaired = re.sub(unquoted_pattern, r'\1: "\2"', repaired)
-            
+
             # Remove trailing commas
-            repaired = re.sub(r',(\s*[}\]])', r'\1', repaired)
-            
+            repaired = re.sub(r",(\s*[}\]])", r"\1", repaired)
+
             json_data = json.loads(repaired)
-            logger.info("JSON repaired successfully", extra={
-                "structured_data": {
-                    "original": args.runcommand,
-                    "repaired": repaired
-                }
-            })
-            print(f"JSON repaired successfully", file=sys.stderr)
+            logger.info(
+                "JSON repaired successfully",
+                extra={
+                    "structured_data": {
+                        "original": args.runcommand,
+                        "repaired": repaired,
+                    }
+                },
+            )
+            print("JSON repaired successfully", file=sys.stderr)
             print(f"Original: {args.runcommand}", file=sys.stderr)
             print(f"Repaired: {repaired}", file=sys.stderr)
         except json.JSONDecodeError as repair_error:
-            logger.error("JSON repair failed", extra={
-                "structured_data": {
-                    "repair_error": str(repair_error),
-                    "original_json": args.runcommand
-                }
-            })
+            logger.error(
+                "JSON repair failed",
+                extra={
+                    "structured_data": {
+                        "repair_error": str(repair_error),
+                        "original_json": args.runcommand,
+                    }
+                },
+            )
             print(f"JSON repair also failed: {repair_error}", file=sys.stderr)
             print(f"Original JSON: {args.runcommand}", file=sys.stderr)
             sys.exit(1)
-    
+
     # Initialize server
     db_path = Path(args.db_path).expanduser()
     cache_dir = Path(args.cache_dir).expanduser()
-    
-    logger.info("Initializing MCP server", extra={
-        "structured_data": {
-            "db_path": str(db_path),
-            "cache_dir": str(cache_dir),
-            "token_limit": args.token_limit
-        }
-    })
-    
+
+    logger.info(
+        "Initializing MCP server",
+        extra={
+            "structured_data": {
+                "db_path": str(db_path),
+                "cache_dir": str(cache_dir),
+                "token_limit": args.token_limit,
+            }
+        },
+    )
+
     server = MCPCodeIndexServer(
-        token_limit=args.token_limit,
-        db_path=db_path,
-        cache_dir=cache_dir
+        token_limit=args.token_limit, db_path=db_path, cache_dir=cache_dir
     )
-    
+
     try:
         logger.debug("Initializing server database connection")
         await server.initialize()
         logger.debug("Server initialized successfully")
-        
+
         # Extract the tool call information from the JSON
         if "method" in json_data and json_data["method"] == "tools/call":
             tool_name = json_data["params"]["name"]
             tool_arguments = json_data["params"]["arguments"]
-            logger.info("JSON-RPC format detected", extra={
-                "structured_data": {
-                    "tool_name": tool_name,
-                    "arguments_keys": list(tool_arguments.keys())
-                }
-            })
+            logger.info(
+                "JSON-RPC format detected",
+                extra={
+                    "structured_data": {
+                        "tool_name": tool_name,
+                        "arguments_keys": list(tool_arguments.keys()),
+                    }
+                },
+            )
         elif "projectName" in json_data and "folderPath" in json_data:
             # Auto-detect: user provided just arguments, try to infer the tool
             if "filePath" in json_data and "description" in json_data:
@@ -267,19 +294,31 @@ async def handle_runcommand(args: argparse.Namespace) -> None:
                 logger.info("Auto-detected tool: check_codebase_size")
                 print("Auto-detected tool: check_codebase_size", file=sys.stderr)
             else:
-                logger.error("Could not auto-detect tool from arguments", extra={
-                    "structured_data": {"provided_keys": list(json_data.keys())}
-                })
-                print("Error: Could not auto-detect tool from arguments. Please use full MCP format:", file=sys.stderr)
-                print('{"method": "tools/call", "params": {"name": "TOOL_NAME", "arguments": {...}}}', file=sys.stderr)
+                logger.error(
+                    "Could not auto-detect tool from arguments",
+                    extra={
+                        "structured_data": {"provided_keys": list(json_data.keys())}
+                    },
+                )
+                print(
+                    "Error: Could not auto-detect tool from arguments. "
+                    "Please use full MCP format:",
+                    file=sys.stderr,
+                )
+                print(
+                    '{"method": "tools/call", "params": '
+                    '{"name": "TOOL_NAME", "arguments": {...}}}',
+                    file=sys.stderr,
+                )
                 sys.exit(1)
         else:
-            logger.error("Invalid JSON format", extra={
-                "structured_data": {"provided_keys": list(json_data.keys())}
-            })
+            logger.error(
+                "Invalid JSON format",
+                extra={"structured_data": {"provided_keys": list(json_data.keys())}},
+            )
             print("Error: JSON must contain a valid MCP tool call", file=sys.stderr)
             sys.exit(1)
-        
+
         # Map tool names to handler methods - use the same mapping as MCP server
         tool_handlers = {
             "get_file_description": server._handle_get_file_description,
@@ -293,30 +332,31 @@ async def handle_runcommand(args: argparse.Namespace) -> None:
             "get_word_frequency": server._handle_get_word_frequency,
             "search_codebase_overview": server._handle_search_codebase_overview,
         }
-        
+
         if tool_name not in tool_handlers:
-            logger.error("Unknown tool requested", extra={
-                "structured_data": {
-                    "tool_name": tool_name,
-                    "available_tools": list(tool_handlers.keys())
-                }
-            })
+            logger.error(
+                "Unknown tool requested",
+                extra={
+                    "structured_data": {
+                        "tool_name": tool_name,
+                        "available_tools": list(tool_handlers.keys()),
+                    }
+                },
+            )
             error_result = {
-                "error": {
-                    "code": -32601,
-                    "message": f"Unknown tool: {tool_name}"
-                }
+                "error": {"code": -32601, "message": f"Unknown tool: {tool_name}"}
             }
             print(json.dumps(error_result, indent=2))
             return
-        
+
         # Clean HTML entities from arguments before execution
         def clean_html_entities(text: str) -> str:
             if not text:
                 return text
             import html
+
             return html.unescape(text)
-        
+
         def clean_arguments(arguments: dict) -> dict:
             cleaned = {}
             for key, value in arguments.items():
@@ -332,56 +372,67 @@ async def handle_runcommand(args: argparse.Namespace) -> None:
                 else:
                     cleaned[key] = value
             return cleaned
-        
+
         cleaned_tool_arguments = clean_arguments(tool_arguments)
-        
-        logger.info("Executing tool", extra={
-            "structured_data": {
-                "tool_name": tool_name,
-                "arguments": {k: v for k, v in cleaned_tool_arguments.items() if k not in ['description']}  # Exclude long descriptions
-            }
-        })
-        
+
+        logger.info(
+            "Executing tool",
+            extra={
+                "structured_data": {
+                    "tool_name": tool_name,
+                    "arguments": {
+                        k: v
+                        for k, v in cleaned_tool_arguments.items()
+                        if k not in ["description"]
+                    },  # Exclude long descriptions
+                }
+            },
+        )
+
         # Execute the tool handler directly
         import time
+
         start_time = time.time()
         result = await tool_handlers[tool_name](cleaned_tool_arguments)
         execution_time = time.time() - start_time
-        
-        logger.info("Tool execution completed", extra={
-            "structured_data": {
-                "tool_name": tool_name,
-                "execution_time_seconds": execution_time,
-                "result_type": type(result).__name__,
-                "result_size": len(json.dumps(result, default=str)) if result else 0
-            }
-        })
-        
+
+        logger.info(
+            "Tool execution completed",
+            extra={
+                "structured_data": {
+                    "tool_name": tool_name,
+                    "execution_time_seconds": execution_time,
+                    "result_type": type(result).__name__,
+                    "result_size": (
+                        len(json.dumps(result, default=str)) if result else 0
+                    ),
+                }
+            },
+        )
+
         print(json.dumps(result, indent=2, default=str))
-        
+
     except Exception as e:
-        logger.error("Tool execution failed", extra={
-            "structured_data": {
-                "tool_name": tool_name if 'tool_name' in locals() else 'unknown',
-                "error_type": type(e).__name__,
-                "error_message": str(e)
-            }
-        })
-        error_result = {
-            "error": {
-                "code": -32603,
-                "message": str(e)
-            }
-        }
+        logger.error(
+            "Tool execution failed",
+            extra={
+                "structured_data": {
+                    "tool_name": tool_name if "tool_name" in locals() else "unknown",
+                    "error_type": type(e).__name__,
+                    "error_message": str(e),
+                }
+            },
+        )
+        error_result = {"error": {"code": -32603, "message": str(e)}}
         print(json.dumps(error_result, indent=2))
     finally:
         # Clean up database connections
-        if hasattr(server, 'db_manager') and server.db_manager:
+        if hasattr(server, "db_manager") and server.db_manager:
             logger.debug("Closing database connections")
             await server.db_manager.close_pool()
             logger.debug("Database connections closed")
         logger.info("=== RUNCOMMAND SESSION ENDED ===")
-        
+
         # Close logger handlers to flush any remaining logs
         for handler in logger.handlers[:]:
             handler.close()
@@ -392,28 +443,27 @@ async def handle_dumpdescriptions(args: argparse.Namespace) -> None:
     """Handle --dumpdescriptions command."""
     from .database.database import DatabaseManager
     from .token_counter import TokenCounter
-    
+
     if len(args.dumpdescriptions) < 1:
         print("Error: Project ID is required", file=sys.stderr)
         sys.exit(1)
-    
+
     project_id = args.dumpdescriptions[0]
     branch = args.dumpdescriptions[1] if len(args.dumpdescriptions) > 1 else None
-    
+
     db_manager = None
     try:
         # Initialize database and token counter
         db_path = Path(args.db_path).expanduser()
         db_manager = DatabaseManager(db_path)
         await db_manager.initialize()
-        
+
         token_counter = TokenCounter(args.token_limit)
-        
+
         # Get file descriptions
         if branch:
             file_descriptions = await db_manager.get_all_file_descriptions(
-                project_id=project_id,
-                branch=branch
+                project_id=project_id, branch=branch
             )
             print(f"File descriptions for project {project_id}, branch {branch}:")
         else:
@@ -421,9 +471,9 @@ async def handle_dumpdescriptions(args: argparse.Namespace) -> None:
                 project_id=project_id
             )
             print(f"File descriptions for project {project_id} (all branches):")
-        
+
         print("=" * 80)
-        
+
         if not file_descriptions:
             print("No descriptions found.")
             total_tokens = 0
@@ -435,71 +485,76 @@ async def handle_dumpdescriptions(args: argparse.Namespace) -> None:
                     print(f"Branch: {desc.branch}")
                 print(f"Description: {desc.description}")
                 print("-" * 40)
-                
+
                 # Count tokens for this description
                 desc_tokens = token_counter.count_file_description_tokens(desc)
                 total_tokens += desc_tokens
-        
+
         print("=" * 80)
         print(f"Total descriptions: {len(file_descriptions)}")
         print(f"Total tokens: {total_tokens}")
-        
+
     finally:
         # Clean up database connections
         if db_manager:
             await db_manager.close_pool()
 
 
-
 async def handle_githook(args: argparse.Namespace) -> None:
     """Handle --githook command."""
     from .logging_config import setup_command_logger
-    
+
     # Set up dedicated logging for githook
     cache_dir = Path(args.cache_dir).expanduser()
     logger = setup_command_logger("githook", cache_dir)
-    
+
     try:
         from .database.database import DatabaseManager
         from .git_hook_handler import GitHookHandler
-        
+
         # Process commit hash arguments
         commit_hashes = args.githook if args.githook else []
-        
-        logger.info("Starting git hook execution", extra={
-            "structured_data": {
-                "args": {
-                    "db_path": str(args.db_path),
-                    "cache_dir": str(args.cache_dir),
-                    "token_limit": args.token_limit,
-                    "commit_hashes": commit_hashes
+
+        logger.info(
+            "Starting git hook execution",
+            extra={
+                "structured_data": {
+                    "args": {
+                        "db_path": str(args.db_path),
+                        "cache_dir": str(args.cache_dir),
+                        "token_limit": args.token_limit,
+                        "commit_hashes": commit_hashes,
+                    }
                 }
-            }
-        })
-        
+            },
+        )
+
         # Initialize database
         db_path = Path(args.db_path).expanduser()
         cache_dir = Path(args.cache_dir).expanduser()
-        
-        logger.info("Setting up directories and database", extra={
-            "structured_data": {
-                "db_path": str(db_path),
-                "cache_dir": str(cache_dir)
-            }
-        })
-        
+
+        logger.info(
+            "Setting up directories and database",
+            extra={
+                "structured_data": {
+                    "db_path": str(db_path),
+                    "cache_dir": str(cache_dir),
+                }
+            },
+        )
+
         # Create directories if they don't exist
         db_path.parent.mkdir(parents=True, exist_ok=True)
         cache_dir.mkdir(parents=True, exist_ok=True)
-        
+
         db_manager = DatabaseManager(db_path)
         await db_manager.initialize()
         logger.debug("Database initialized successfully")
-        
+
         # Initialize git hook handler
         git_handler = GitHookHandler(db_manager, cache_dir, logger)
         logger.debug("Git hook handler initialized")
-        
+
         # Run git hook analysis
         logger.info("Starting git hook analysis")
         if len(commit_hashes) == 0:
@@ -510,31 +565,36 @@ async def handle_githook(args: argparse.Namespace) -> None:
             await git_handler.run_githook_mode(commit_hash=commit_hashes[0])
         elif len(commit_hashes) == 2:
             # Process commit range
-            await git_handler.run_githook_mode(commit_range=(commit_hashes[0], commit_hashes[1]))
+            await git_handler.run_githook_mode(
+                commit_range=(commit_hashes[0], commit_hashes[1])
+            )
         else:
             raise ValueError("--githook accepts 0, 1, or 2 commit hashes")
         logger.info("Git hook analysis completed successfully")
-        
+
     except Exception as e:
-        logger.error("Git hook execution failed", extra={
-            "structured_data": {
-                "error_type": type(e).__name__,
-                "error_message": str(e)
-            }
-        })
+        logger.error(
+            "Git hook execution failed",
+            extra={
+                "structured_data": {
+                    "error_type": type(e).__name__,
+                    "error_message": str(e),
+                }
+            },
+        )
         print(f"Git hook error: {e}", file=sys.stderr)
         sys.exit(1)
     finally:
         # Clean up database connections
-        if 'db_manager' in locals():
+        if "db_manager" in locals():
             try:
                 await db_manager.close_pool()
                 logger.debug("Database connections closed")
             except Exception as e:
                 logger.warning(f"Error closing database connections: {e}")
-        
+
         logger.info("=== GITHOOK SESSION ENDED ===")
-        
+
         # Close logger handlers to flush any remaining logs
         for handler in logger.handlers[:]:
             handler.close()
@@ -544,50 +604,57 @@ async def handle_githook(args: argparse.Namespace) -> None:
 async def handle_cleanup(args: argparse.Namespace) -> None:
     """Handle --cleanup command."""
     from .logging_config import setup_command_logger
-    
+
     # Set up dedicated logging for cleanup
     cache_dir = Path(args.cache_dir).expanduser()
     logger = setup_command_logger("cleanup", cache_dir)
-    
+
     db_manager = None
     try:
         from .database.database import DatabaseManager
-        
-        logger.info("Starting database cleanup", extra={
-            "structured_data": {
-                "args": {
-                    "db_path": str(args.db_path),
-                    "cache_dir": str(args.cache_dir)
+
+        logger.info(
+            "Starting database cleanup",
+            extra={
+                "structured_data": {
+                    "args": {
+                        "db_path": str(args.db_path),
+                        "cache_dir": str(args.cache_dir),
+                    }
                 }
-            }
-        })
-        
+            },
+        )
+
         # Initialize database
         db_path = Path(args.db_path).expanduser()
         db_manager = DatabaseManager(db_path)
         await db_manager.initialize()
         logger.debug("Database initialized successfully")
-        
+
         # Perform cleanup
         logger.info("Removing empty projects")
         removed_count = await db_manager.cleanup_empty_projects()
-        
+
         if removed_count > 0:
             print(f"Removed {removed_count} empty project(s)")
-            logger.info("Cleanup completed", extra={
-                "structured_data": {"removed_projects": removed_count}
-            })
+            logger.info(
+                "Cleanup completed",
+                extra={"structured_data": {"removed_projects": removed_count}},
+            )
         else:
             print("No empty projects found")
             logger.info("No empty projects found")
-        
+
     except Exception as e:
-        logger.error("Cleanup failed", extra={
-            "structured_data": {
-                "error_type": type(e).__name__,
-                "error_message": str(e)
-            }
-        })
+        logger.error(
+            "Cleanup failed",
+            extra={
+                "structured_data": {
+                    "error_type": type(e).__name__,
+                    "error_message": str(e),
+                }
+            },
+        )
         print(f"Cleanup error: {e}", file=sys.stderr)
         sys.exit(1)
     finally:
@@ -597,7 +664,7 @@ async def handle_cleanup(args: argparse.Namespace) -> None:
             await db_manager.close_pool()
             logger.debug("Database connections closed")
         logger.info("=== CLEANUP SESSION ENDED ===")
-        
+
         # Close logger handlers to flush any remaining logs
         for handler in logger.handlers[:]:
             handler.close()
@@ -607,72 +674,82 @@ async def handle_cleanup(args: argparse.Namespace) -> None:
 async def handle_map(args: argparse.Namespace) -> None:
     """Handle --map command."""
     from .logging_config import setup_command_logger
-    import re
-    from collections import defaultdict
-    from pathlib import Path as PathLib
-    
+
     # Set up dedicated logging for map
     cache_dir = Path(args.cache_dir).expanduser()
     logger = setup_command_logger("map", cache_dir)
-    
+
     db_manager = None
     try:
         from .database.database import DatabaseManager
-        
-        logger.info("Starting project map generation", extra={
-            "structured_data": {
-                "project_identifier": args.map,
-                "args": {
-                    "db_path": str(args.db_path),
-                    "cache_dir": str(args.cache_dir)
+
+        logger.info(
+            "Starting project map generation",
+            extra={
+                "structured_data": {
+                    "project_identifier": args.map,
+                    "args": {
+                        "db_path": str(args.db_path),
+                        "cache_dir": str(args.cache_dir),
+                    },
                 }
-            }
-        })
-        
+            },
+        )
+
         # Initialize database
         db_path = Path(args.db_path).expanduser()
         db_manager = DatabaseManager(db_path)
         await db_manager.initialize()
         logger.debug("Database initialized successfully")
-        
+
         # Get project data
         logger.info("Retrieving project data")
         project_data = await db_manager.get_project_map_data(args.map)
-        
+
         if not project_data:
             print(f"Error: Project '{args.map}' not found", file=sys.stderr)
-            logger.error("Project not found", extra={"structured_data": {"identifier": args.map}})
+            logger.error(
+                "Project not found", extra={"structured_data": {"identifier": args.map}}
+            )
             sys.exit(1)
-        
-        project = project_data['project']
-        branch = project_data['branch']
-        overview = project_data['overview']
-        files = project_data['files']
-        
-        logger.info("Generating markdown map", extra={
-            "structured_data": {
-                "project_name": project.name,
-                "branch": branch,
-                "file_count": len(files),
-                "has_overview": overview is not None
-            }
-        })
-        
+
+        project = project_data["project"]
+        branch = project_data["branch"]
+        overview = project_data["overview"]
+        files = project_data["files"]
+
+        logger.info(
+            "Generating markdown map",
+            extra={
+                "structured_data": {
+                    "project_name": project.name,
+                    "branch": branch,
+                    "file_count": len(files),
+                    "has_overview": overview is not None,
+                }
+            },
+        )
+
         # Generate markdown
-        markdown_content = generate_project_markdown(project, branch, overview, files, logger)
-        
+        markdown_content = generate_project_markdown(
+            project, branch, overview, files, logger
+        )
+
         # Output the markdown
         print(markdown_content)
-        
+
         logger.info("Project map generated successfully")
-        
+
     except Exception as e:
-        logger.error("Map generation failed", extra={
-            "structured_data": {
-                "error_type": type(e).__name__,
-                "error_message": str(e)
-            }
-        })
+        logger.error(
+            "Map generation failed",
+            extra={
+                "structured_data": {
+                    "error_type": type(e).__name__,
+                    "error_message": str(e),
+                }
+            },
+        )
         print(f"Map generation error: {e}", file=sys.stderr)
         sys.exit(1)
     finally:
@@ -682,7 +759,7 @@ async def handle_map(args: argparse.Namespace) -> None:
             await db_manager.close_pool()
             logger.debug("Database connections closed")
         logger.info("=== MAP SESSION ENDED ===")
-        
+
         # Close logger handlers to flush any remaining logs
         for handler in logger.handlers[:]:
             handler.close()
@@ -694,38 +771,40 @@ def generate_project_markdown(project, branch, overview, files, logger):
     import re
     from collections import defaultdict
     from pathlib import Path as PathLib
-    
+
     markdown_lines = []
-    
+
     # Project header with sentence case
     project_name = project.name.title() if project.name.islower() else project.name
     markdown_lines.append(f"# {project_name}")
     markdown_lines.append("")
-    
+
     # Project metadata
     markdown_lines.append(f"**Branch:** {branch}")
     markdown_lines.append("")
-    
+
     # Project overview (with header demotion if needed)
     if overview and overview.overview:
         markdown_lines.append("## Project Overview")
         markdown_lines.append("")
-        
+
         # Check if overview contains H1 headers and demote if needed
         overview_content = overview.overview
-        if re.search(r'^#\s', overview_content, re.MULTILINE):
+        if re.search(r"^#\s", overview_content, re.MULTILINE):
             logger.debug("H1 headers found in overview, demoting all headers")
             # Demote all headers by one level
-            overview_content = re.sub(r'^(#{1,6})', r'#\1', overview_content, flags=re.MULTILINE)
-        
+            overview_content = re.sub(
+                r"^(#{1,6})", r"#\1", overview_content, flags=re.MULTILINE
+            )
+
         markdown_lines.append(overview_content)
         markdown_lines.append("")
-    
+
     # File structure
     if files:
         markdown_lines.append("## Codebase Structure")
         markdown_lines.append("")
-        
+
         # Organize files by directory
         directories = defaultdict(list)
         for file_desc in files:
@@ -737,13 +816,15 @@ def generate_project_markdown(project, branch, overview, files, logger):
                 # File in subdirectory
                 directory = str(file_path.parent)
                 directories[directory].append(file_desc)
-        
+
         # Sort directories (root first, then alphabetically)
-        sorted_dirs = sorted(directories.keys(), key=lambda x: ("" if x == "(root)" else x))
-        
+        sorted_dirs = sorted(
+            directories.keys(), key=lambda x: ("" if x == "(root)" else x)
+        )
+
         for directory in sorted_dirs:
             dir_files = directories[directory]
-            
+
             # Directory header
             if directory == "(root)":
                 markdown_lines.append("### Root Directory")
@@ -752,104 +833,108 @@ def generate_project_markdown(project, branch, overview, files, logger):
                 depth = len(PathLib(directory).parts)
                 header_level = "#" * min(depth + 2, 6)  # Cap at H6
                 markdown_lines.append(f"{header_level} {directory}/")
-            
+
             markdown_lines.append("")
-            
+
             # Files table
             markdown_lines.append("| File | Description |")
             markdown_lines.append("|------|-------------|")
-            
+
             for file_desc in sorted(dir_files, key=lambda x: x.file_path):
                 file_name = PathLib(file_desc.file_path).name
                 # Escape pipe characters in descriptions for markdown table
-                description = file_desc.description.replace("|", "\\|").replace("\n", " ").strip()
+                description = (
+                    file_desc.description.replace("|", "\\|").replace("\n", " ").strip()
+                )
                 markdown_lines.append(f"| `{file_name}` | {description} |")
-            
+
             markdown_lines.append("")
-    
+
     # Footer with generation info
     from datetime import datetime
+
     timestamp = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
     markdown_lines.append("---")
     markdown_lines.append(f"*Generated by MCP Code Indexer on {timestamp}*")
-    
+
     return "\n".join(markdown_lines)
 
 
 async def main() -> None:
     """Main entry point for the MCP server."""
     args = parse_arguments()
-    
-    # Handle git hook command  
+
+    # Handle git hook command
     if args.githook is not None:
         await handle_githook(args)
         return
-    
+
     # Handle utility commands
     if args.getprojects:
         await handle_getprojects(args)
         return
-    
+
     if args.runcommand:
         await handle_runcommand(args)
         return
-    
+
     if args.dumpdescriptions:
         await handle_dumpdescriptions(args)
         return
-    
+
     if args.cleanup:
         await handle_cleanup(args)
         return
-    
+
     if args.map:
         await handle_map(args)
         return
-    
+
     # Setup structured logging
-    log_file = Path(args.cache_dir).expanduser() / "server.log" if args.cache_dir else None
+    log_file = (
+        Path(args.cache_dir).expanduser() / "server.log" if args.cache_dir else None
+    )
     logger = setup_logging(
-        log_level=args.log_level,
-        log_file=log_file,
-        enable_file_logging=True
+        log_level=args.log_level, log_file=log_file, enable_file_logging=True
     )
-    
+
     # Setup error handling
     error_handler = setup_error_handling(logger)
-    
+
     # Expand user paths
     db_path = Path(args.db_path).expanduser()
     cache_dir = Path(args.cache_dir).expanduser()
-    
+
     # Create directories if they don't exist
     db_path.parent.mkdir(parents=True, exist_ok=True)
     cache_dir.mkdir(parents=True, exist_ok=True)
-    
+
     # Log startup information to stderr (stdout reserved for MCP JSON-RPC)
-    logger.info("Starting MCP Code Index Server", extra={
-        "structured_data": {
-            "startup": {
-                "version": __version__,
-                "token_limit": args.token_limit,
-                "db_path": str(db_path),
-                "cache_dir": str(cache_dir),
-                "log_level": args.log_level
+    logger.info(
+        "Starting MCP Code Index Server",
+        extra={
+            "structured_data": {
+                "startup": {
+                    "version": __version__,
+                    "token_limit": args.token_limit,
+                    "db_path": str(db_path),
+                    "cache_dir": str(cache_dir),
+                    "log_level": args.log_level,
+                }
             }
-        }
-    })
-    
+        },
+    )
+
     try:
         # Import and run the MCP server
         from .server.mcp_server import MCPCodeIndexServer
-        
+
         server = MCPCodeIndexServer(
-            token_limit=args.token_limit,
-            db_path=db_path,
-            cache_dir=cache_dir
+            token_limit=args.token_limit, db_path=db_path, cache_dir=cache_dir
         )
-        
+
         await server.run()
-        
+
     except Exception as e:
         error_handler.log_error(e, context={"phase": "startup"})
         raise
@@ -866,6 +951,7 @@ def cli_main():
     except Exception as e:
         # Log critical errors to stderr, not stdout
         import traceback
+
         print(f"Server failed to start: {e}", file=sys.stderr)
         print(f"Traceback: {traceback.format_exc()}", file=sys.stderr)
         sys.exit(1)