MCP File System Server

A simple Model Context Protocol (MCP) server providing file system operations. This server offers a clean API for performing file system operations within a specified project directory, following the MCP protocol design.

Overview

This MCP server enables AI assistants like Claude (via Claude Desktop) or other MCP-compatible systems to interact with your local file system. With these capabilities, AI assistants can:

• Read your existing code and project files
• Write new files with generated content
• Update and modify existing files with precision using exact string matching
• Make selective edits to code without rewriting entire files
• Delete files when needed
• Review repositories to provide analysis and recommendations
• Debug and fix issues in your codebase
• Generate complete implementations based on your specifications

All operations are securely contained within your specified project directory, giving you control while enabling powerful AI collaboration on your local files.

By connecting your AI assistant to your filesystem, you can transform your workflow from manual coding to a more intuitive prompting approach - describe what you need in natural language and let the AI generate, modify, and organize code directly in your project files.

Features

• list_directory: List all files and directories in the project directory
• read_file: Read the contents of a file
• save_file: Write content to a file atomically
• append_file: Append content to the end of a file
• delete_this_file: Delete a specified file from the filesystem
• edit_file: Make selective edits using exact string matching
• move_file: Move or rename files and directories within the project
• get_reference_projects: Discover available reference projects
• list_reference_directory: List files in reference projects
• read_reference_file: Read files from reference projects
• Structured Logging: Comprehensive logging system with both human-readable and JSON formats

Installation

# Clone the repository
git clone https://github.com/MarcusJellinghaus/mcp_server_filesystem.git
cd mcp_server_filesystem

# Create and activate a virtual environment (optional but recommended)
python -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate

# Install dependencies using pip with pyproject.toml
pip install -e .

Running the Server

Once installed, you can use the mcp-server-filesystem command directly:

mcp-server-filesystem --project-dir /path/to/project [--reference-project NAME=/path/to/reference]... [--log-level LEVEL] [--log-file PATH]

Command Line Arguments:

• --project-dir: (Required) Directory to serve files from
• --reference-project: (Optional) Add reference project in format name=/path/to/dir (repeatable, auto-renames duplicates)
• --log-level: (Optional) Set logging level (DEBUG, INFO, WARNING, ERROR, CRITICAL)
• --log-file: (Optional) Path for structured JSON logs. If not specified, logs to mcp_filesystem_server_{timestamp}.log in project_dir/logs/.

The server uses FastMCP for operation. The project directory parameter (--project-dir) is required for security reasons. All file operations will be restricted to this directory. Attempts to access files outside this directory will result in an error.

Structured Logging

The server provides flexible logging options:

• Standard human-readable logs to console
• Structured JSON logs to file (default: project_dir/logs/mcp_filesystem_server_{timestamp}.log or custom path with --log-file)
• Function call tracking with parameters, timing, and results
• Automatic error context capture
• Configurable log levels (DEBUG, INFO, WARNING, ERROR, CRITICAL)
• Use --console-only to disable file logging

Reference Projects

Reference projects allow you to provide AI assistants with read-only access to additional codebases or directories for context and reference. This feature enables the LLM to browse and read files from multiple projects while maintaining write access only to the main project directory.

Features

• Read-only access: Reference projects can only be browsed and read from, never modified
• Multiple projects: Configure multiple reference projects simultaneously
• Auto-discovery: LLM can discover available reference projects
• Security: Same path validation and gitignore filtering as main project
• Flexible paths: Supports both relative and absolute paths

Configuration

Use the --reference-project argument to add reference projects:

# Single reference project
mcp-server-filesystem --project-dir ./my-project --reference-project docs=./documentation

# Multiple reference projects
mcp-server-filesystem --project-dir ./my-project \
  --reference-project docs=./documentation \
  --reference-project examples=/home/user/examples \
  --reference-project libs=../shared-libraries

# Absolute paths
mcp-server-filesystem --project-dir /path/to/main/project \
  --reference-project utils=/usr/local/utils \
  --reference-project config=/etc/myapp

Auto-Rename Behavior

If you specify duplicate reference project names, they are automatically renamed with numeric suffixes:

# This configuration:
mcp-server-filesystem --project-dir ./project \
  --reference-project docs=./docs1 \
  --reference-project docs=./docs2 \
  --reference-project docs=./docs3

# Results in these reference project names:
# - docs (points to ./docs1)
# - docs_2 (points to ./docs2)  
# - docs_3 (points to ./docs3)

Startup Validation

The server validates reference projects at startup:

• Valid references: Added successfully and available to the LLM
• Invalid references: Logged as warnings, but server continues with valid ones
• Path resolution: Relative paths are resolved relative to the current working directory

Use Cases

• Documentation browsing: Give the LLM access to project documentation or wikis
• Code examples: Reference example projects or templates
• Shared libraries: Browse common utility libraries or frameworks
• Configuration files: Access system or application configuration directories
• Multi-project development: Work on one project while referencing related projects

Security Notes

• Reference projects are strictly read-only - no write, edit, or delete operations are possible
• All paths are validated to prevent directory traversal attacks
• Gitignore filtering is automatically applied to hide irrelevant files
• Path access is restricted to the specified reference project directories

Integration Options

This server can be integrated with different Claude interfaces. Each requires a specific configuration.

Claude Desktop App Integration

The Claude Desktop app can also use this file system server.

Configuration Steps for Claude Desktop

1. Locate the Claude Desktop configuration file:

   • Windows: %APPDATA%\Claude\claude_desktop_config.json
   • macOS: ~/Library/Application Support/Claude/claude_desktop_config.json

2. Add the MCP server configuration (create the file if it doesn't exist):

{
  "mcpServers": {
    "filesystem": {
      "command": "mcp-server-filesystem",
      "args": [
        "--project-dir",
        "C:\\path\\to\\your\\specific\\project",
        "--reference-project",
        "docs=C:\\path\\to\\documentation",
        "--reference-project",
        "examples=C:\\path\\to\\examples",
        "--log-level",
        "INFO"
      ]
    }
  }
}

1. Configuration notes:

   • The mcp-server-filesystem command should be available in your PATH after installation
   • You must specify an explicit project directory path in --project-dir
   • Replace the project directory path with your actual project path
   • The project directory should be the folder you want Claude to access

2. Restart the Claude Desktop app to apply changes

Troubleshooting Claude Desktop Integration

• Check logs at: %APPDATA%\Claude\logs (Windows) or ~/Library/Application Support/Claude/logs (macOS)
• Verify the mcp-server-filesystem command is available in your PATH (run mcp-server-filesystem --help to test)
• Ensure the specified project directory exists and is accessible
• Verify all paths in your configuration are correct

Contributing

For development setup, testing, and contribution guidelines, see CONTRIBUTING.md.

Available Tools

The server exposes the following MCP tools:

Operation	Description	Example Prompt
list_directory	Lists files and directories in the project directory	"List all files in the src directory"
read_file	Reads the contents of a file	"Show me the contents of main.js"
save_file	Creates or overwrites files atomically	"Create a new file called app.js"
append_file	Adds content to existing files	"Add a function to utils.js"
delete_this_file	Removes files from the filesystem	"Delete the temporary.txt file"
edit_file	Makes selective edits using exact string matching	"Fix the bug in the fetch function"
move_file	Moves or renames files and directories	"Rename config.js to settings.js"
get_reference_projects	Lists available reference projects	"What reference projects are available?"
list_reference_directory	Lists files in a reference project	"List files in the docs reference project"
read_reference_file	Reads files from reference projects	"Show me the README from the examples project"

Tool Details

List Directory

• Returns a list of file and directory names
• By default, results are filtered based on .gitignore patterns and .git folders are excluded

Read File

• Parameters: file_path (string): Path to the file to read (relative to project directory)
• Returns the content of the file as a string

Save File

• Parameters:
  • file_path (string): Path to the file to write to
  • content (string): Content to write to the file
• Returns a boolean indicating success

Append File

• Parameters:
  • file_path (string): Path to the file to append to
  • content (string): Content to append to the file
• Returns a boolean indicating success
• Note: The file must already exist; use save_file to create new files

Delete This File

• Parameters: file_path (string): Path to the file to delete
• Returns a boolean indicating success
• Note: This operation is irreversible and will permanently remove the file

Edit File

Makes precise edits to files using exact string matching. This tool is designed for reliability and predictability.

Parameters:

• file_path (string): File to edit (relative to project directory)
• edits (array): List of edit operations, each containing:
  • old_text (string): Exact text to find and replace (must match exactly)
  • new_text (string): Replacement text
• dry_run (boolean, optional): Preview changes without applying (default: False)
• options (object, optional): Formatting settings
  • preserve_indentation (boolean, default: False): Apply indentation from old_text to new_text

Key Characteristics:

• Exact string matching only - The old_text must match exactly (case-sensitive, whitespace-sensitive)
• No fuzzy or partial matching - For maximum reliability and predictability
• First occurrence replacement - Only replaces the first match of each old_text pattern
• Sequential processing - Edits are applied in order, with each edit seeing the results of previous edits
• Already-applied detection - Automatically detects when edits are already applied (no-op optimization)
• Git-style diff output - Shows exactly what changed in unified diff format
• Clear error reporting - Specific messages when text patterns are not found

Examples:

# Basic text replacement
edit_file("config.py", [
    {"old_text": "DEBUG = False", "new_text": "DEBUG = True"}
])

# Multiple edits in one operation
edit_file("app.py", [
    {"old_text": "def old_function():", "new_text": "def new_function():"},
    {"old_text": "old_function()", "new_text": "new_function()"}
])

# Preview changes without applying
edit_file("code.py", edits, dry_run=True)

# With indentation preservation
edit_file("indented.py", [
    {"old_text": "    old_code()", "new_text": "new_code()"}
], options={"preserve_indentation": True})

Important Notes:

• The text in old_text must match exactly - including spacing, capitalization, and line breaks
• Use \n for line breaks in multi-line replacements
• If old_text appears multiple times, only the first occurrence is replaced
• Consider using dry_run=True to preview changes before applying them

Move File

Moves or renames files and directories within the project directory. Automatically preserves git history when applicable.

Parameters:

• source_path (string): Source file/directory path (relative to project)
• destination_path (string): Destination path (relative to project)

Returns: Boolean (true for success)

Features:

• Automatically creates parent directories if they don't exist
• Preserves git history when moving tracked files (uses git mv internally)
• Falls back to filesystem operations if git is unavailable
• Works for both files and directories
• Simple, clear error messages for LLMs

Examples:

# Rename a file
move_file("old_name.py", "new_name.py")

# Move a file to a different directory
move_file("src/temp.py", "archive/temp.py")

# Rename a directory
move_file("old_folder", "new_folder")

# Move with automatic parent directory creation
move_file("file.txt", "new_dir/sub_dir/file.txt")  # Creates new_dir/sub_dir if needed

Error Handling:

• Returns simplified error messages suitable for AI assistants:
  • "File not found" - when source doesn't exist
  • "Destination already exists" - when target path is occupied
  • "Permission denied" - for access issues
  • "Invalid path" - for security violations
  • "Move operation failed" - for unexpected errors

Get Reference Projects

Discovery tool for LLMs to find available reference projects.

Parameters: None

Returns: Dictionary containing:

• count: Number of available projects
• projects: List of project names
• usage: Instructions for next steps

Example:

get_reference_projects()
# Returns: {
#   "count": 3,
#   "projects": ["docs", "examples", "utils"],
#   "usage": "Use these 3 projects with list_reference_directory() and read_reference_file()"
# }

Use Cases:

• LLM discovers what reference projects are available
• Initial exploration of additional codebases
• Dynamic selection of reference projects to browse

List Reference Directory

Lists files and directories in a reference project, with the same gitignore filtering as the main project.

Parameters:

• reference_name (string): Name of the reference project

Returns: List of strings containing file and directory names

Examples:

# List root directory of reference project (shows subdirectories)
list_reference_directory("docs")

# Then read files from subdirectories using read_reference_file
read_reference_file("examples", "src/components/Button.tsx")

Features:

• Automatic gitignore filtering (same as main project)
• Excludes .git directories
• Returns relative paths within the reference project
• Validates reference project exists

Read Reference File

Reads the contents of a file from a reference project.

Parameters:

• reference_name (string): Name of the reference project
• file_path (string): Path to the file within the reference project (relative to reference project root)

Returns: String containing the file contents

Examples:

# Read README from docs reference project
read_reference_file("docs", "README.md")

# Read source file from examples project
read_reference_file("examples", "src/app.py")

# Read config file
read_reference_file("config", "settings/production.yml")

Features:

• Read-only access (no modification possible)
• Same path validation as main project files
• Supports any text-based file format
• Returns raw file contents as string

Error Handling:

• "Reference project not found" - when reference_name doesn't exist
• "File not found" - when file doesn't exist in reference project
• "Invalid path" - for security violations or path traversal attempts
• "Permission denied" - for access issues

Security Features

• All paths are normalized and validated to ensure they remain within the project directory
• Reference projects use the same path validation and security measures
• Path traversal attacks are prevented for both main project and reference projects
• Files are written atomically to prevent data corruption
• Delete operations are restricted to the project directory for safety
• Reference projects are strictly read-only to prevent accidental modifications

MCP Configuration Management Tool

For easy configuration and installation of this MCP server, you can use the mcp-config development tool. This CLI tool simplifies the process of managing MCP server configurations across multiple clients (Claude Desktop, VS Code, etc.).

Installation

# Install mcp-config
pip install git+https://github.com/MarcusJellinghaus/mcp-config.git

Quick Setup

# Setup for Claude Desktop with automatic configuration
mcp-config setup mcp-server-filesystem "Filesystem Server" --project-dir /path/to/your/project

# Setup with reference projects
mcp-config setup mcp-server-filesystem "Filesystem Server" \
  --project-dir /path/to/your/project \
  --reference-project docs=/path/to/documentation \
  --reference-project examples=/path/to/examples

# Setup with custom log configuration
mcp-config setup mcp-server-filesystem "Filesystem Server" \
  --project-dir /path/to/your/project \
  --reference-project utils=/shared/utilities \
  --log-level DEBUG \
  --log-file /custom/path/server.log

Learn more: mcp-config on GitHub

This tool eliminates the manual configuration steps and reduces setup errors by handling path resolution, environment detection, and client-specific configuration formats automatically.

License

This project is licensed under the MIT License - see the LICENSE file for details.

The MIT License is a permissive license that allows reuse with minimal restrictions. It permits use, copying, modification, and distribution with proper attribution.

Links

• MCP Python SDK
• MCP Python Code Checker
• MCP Configuration Tool
• Cline MCP Servers Documentation
• Cline Extension for VSCode
• Model Context Protocol Documentation