MCP Workspace README

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.

Path Confinement

Every path is validated against the project directory before any file operation. Validation resolves symlinks and rejects the path if the resolved location lies outside the project directory. A .. segment is rejected outright rather than followed. Reference projects are validated the same way against their own directory.

Two kinds of path are rejected that earlier versions accepted:

• A .. segment anywhere in the path, not only a leading one. read_file("src/../README.md") is rejected; use read_file("README.md").
• A path that leaves the project through a symlink. A symlinked file inside the project whose target is outside it, or an intermediate symlinked directory component, is rejected even though the path contains no ... To read content that lives outside the project, configure it with --reference-project (read-only) or run a second server instance pointed at it.

One limitation: if the operating system cannot resolve a path at all, validation falls back to the lexical checks alone — the path must contain no .. and must lie under the project directory by name — so a symlink pointing outside the project is not detected in that case.

Features

• list_directory: List all files and directories in the project directory
• read_file: Read a file, or a line slice via start_line/end_line.
• save_file: Write a file, creating parent directories as needed.
• append_file: Append content to the end of a file
• delete_this_file: Delete a single specified file from the filesystem
• delete_directory: Delete a directory (empty by default, whole tree with recursive=True)
• edit_file: Edit a file by exact string match; replace_all for multiple matches.
• move_file: Move or rename files and directories (git-aware: uses git mv for tracked files, else filesystem move)
• get_reference_projects: Discover available reference projects
• list_reference_directory: List files in reference projects
• read_reference_file: Read a reference-project file, or a line slice via start_line/end_line.
• Cross-repo GitHub access: the GitHub issue, pull request, search and label read tools accept reference_name; issues can also be created, edited and commented on
• Structured Logging: Comprehensive logging system with both human-readable and JSON formats

Installation

# Clone the repository
git clone https://github.com/MarcusJellinghaus/mcp-workspace.git
cd mcp_workspace

# 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-workspace command directly:

mcp-workspace --project-dir /path/to/project [--reference-project NAME=/path/to/reference]... [--log-level LEVEL] [--log-file PATH] [--file-size-limit N] [--fail-on-reviews] [--enforce-base-branch-format]

Command Line Arguments:

• --project-dir: Directory to serve files from. The server exits with code 1 if it is missing or not a valid directory.
• --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_workspace_{timestamp}.log in project_dir/logs/.
• --file-size-limit: (Optional) Default line limit for check_file_size when max_lines is omitted; must be > 0. Falls back to 600 when not set.
• --fail-on-reviews: (Optional) Default for check_branch_status' review gate; the tool parameter overrides per call. Off unless set.
• --enforce-base-branch-format / --no-enforce-base-branch-format: (Optional) Reject a malformed ### Base Branch section (more than one line) when creating or editing an issue body, in github_issue_create and github_issue_edit. On by default.

Unrecognized arguments are ignored at startup rather than stopping the server; each one is logged as a WARNING, plus a startup INFO line summarizing them. Abbreviated flags such as --project are no longer accepted as prefixes of --project-dir; they are treated as unknown arguments and ignored.

Startup errors are written to stderr and, when no normal log is available, to logs/mcp_workspace_startup_error.log in the working directory.

The server uses FastMCP for operation. All file operations are restricted to the --project-dir directory for security reasons, and attempts to access files outside it result in an error.

GitHub configuration

GitHub settings are read from ~/.mcp_coder/config.toml (the user app-data directory of mcp_coder), section [github]:

• token: GitHub token. The GITHUB_TOKEN environment variable takes precedence.
• test_repo_url: repository used by integration tests. The GITHUB_TEST_REPO_URL environment variable takes precedence.
• trusted_commenters: list of GitHub logins whose comments are shown to the agent. There is no environment-variable override.

[github]
token = "ghp_..."
trusted_commenters = ["dependabot[bot]"]

Commenter trust

check_branch_status and github_pr_view show PR and issue text only from trusted authors:

• An author is trusted if their GitHub association is OWNER, MEMBER or COLLABORATOR, or their login is in trusted_commenters (case-insensitive; include the [bot] suffix, e.g. dependabot[bot]).
• Everything else is withheld from the output and replaced by a count line.
• Roles are relative to the repository being read, including with reference_name.
• The allowlist lives outside the repository on purpose, so a PR cannot add itself.

Structured Logging

The server provides flexible logging options:

• Standard human-readable logs to console
• Structured JSON logs to file (default: project_dir/logs/mcp_workspace_{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 file access to additional codebases or directories for context and reference. This feature enables the LLM to browse and read files from multiple projects while keeping file writes restricted to the main project directory. A reference project with a configured repository URL can also be reached through the GitHub tools — see Cross-Repo GitHub Access.

Features

• Read-only file access: Reference project files can only be browsed and read from, never modified. Their GitHub issues are a separate matter — see Cross-Repo GitHub Access
• 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-workspace --project-dir ./my-project --reference-project docs=./documentation

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

# Absolute paths
mcp-workspace --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-workspace --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 project files are strictly read-only - no write, edit, or delete file 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
• The same rejections described in Path Confinement apply to reference-project paths

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-workspace",
      "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"
      ]
    }
  }
}

3. Configuration notes:

   • The mcp-workspace 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

4. 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-workspace command is available in your PATH (run mcp-workspace --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:

Tool Details

List Directory

• Returns a list of file and directory names
• The .gitignore in the listed directory is applied; no other .gitignore file is read — including the project-root one when listing a subdirectory — nor .git/info/exclude
• .git folders are excluded

Read File

• Parameters:
  • file_path (string): Path to the file to read (relative to project directory)
  • start_line (integer, optional): First line to return (1-based, inclusive). Must be provided together with end_line.
  • end_line (integer, optional): Last line to return (1-based, inclusive). Must be provided together with start_line.
  • with_line_numbers (boolean, optional): Prefix each line with its line number. Defaults to True when a line range is specified, False for full reads.
• 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

Delete Directory

Deletes a directory within the project directory.

Parameters:

• dir_path (string): Path to the directory to delete (relative to project)
• recursive (boolean, optional): Delete the whole tree when True (default: False)

Features:

• Deletes an empty directory by default (recursive=False)
• recursive=True deletes the whole tree, including its contents (via shutil.rmtree)
• Handles directories only - use delete_this_file for files
• Idempotent: deleting a missing directory returns a message, not an error
• Refuses to delete the project root
• Enforces .gitignore on the top-level path; a recursive delete still removes individually-gitignored children (e.g. nested __pycache__/)
• Returns the list of deleted paths (capped at 20 entries with a summary line)

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 {"name": ..., "url": ...} objects. url is the configured repository URL — a project with url: null still works with the reference file tools, but not with the GitHub tools.
• usage: Instructions for next steps

Example:

get_reference_projects()
# Returns: {
#   "count": 3,
#   "projects": [{"name": "docs", "url": "https://github.com/org/docs"}, ...],
#   "usage": "Pass a name as reference_name to the reference file tools, git(), and the GitHub read tools; issues can also be created, edited and commented on"
# }

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)
• start_line (integer, optional): First line to return (1-based, inclusive). Must be provided together with end_line.
• end_line (integer, optional): Last line to return (1-based, inclusive). Must be provided together with start_line.
• with_line_numbers (boolean, optional): Prefix each line with its line number. Defaults to True when a line range is specified, False for full reads.

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 specific lines with line numbers
read_reference_file("examples", "src/app.py", start_line=10, end_line=20)

# 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

Cross-Repo GitHub Access

The GitHub tools that take an optional reference_name act on the workspace repository without it, and on the named reference project with it. Issues, pull requests, searches and labels can be read there; issues can also be created, edited and commented on.

Features:

• The repository is resolved from the reference project's configured URL — no clone is performed, so a URL-only reference project works
• Only names listed by get_reference_projects() are accepted; arbitrary owner/repo strings are not
• Any GitHub tool without a reference_name parameter targets the workspace repository
• Workflow status-* labels are rejected on both sides, for every repository, and mcp-coder gh-tool set-status acts on the current checkout — so a sibling repo's issue can only be advanced through its status workflow from that repo's own checkout

Error Handling: returned as "Error: ..." strings rather than raised:

• "Error: Reference project '<name>' not found" - when the name is not a reference project
• "Error: Reference project '<name>' has no URL configured" - when the reference project has no repository URL

Check File Size

Reports files whose line count exceeds a threshold.

Parameters:

• max_lines (integer, optional): Line threshold. Falls back to the server's --file-size-limit flag, then to 600

Features:

• Counts lines in every UTF-8 file under the project directory — all file types, tracked or not — excluding .git/ and anything the project-root .gitignore matches. Nested .gitignore files are not read
• Files listed in .large-files-allowlist (one path per line, # comments allowed) are exempt; entries are matched as exact paths, not globs
• Allowlist entries are reported as stale when the file no longer exceeds the threshold, and also when it is missing, binary/non-UTF-8, or matched by .gitignore — for example after a rename or a typo in the entry
• The violations list and the stale-entries list are each capped at 50 with a showing X of Y notice; the caps are internal and there is no parameter to lift them

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 project files 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-workspace "Filesystem Server" --project-dir /path/to/your/project

# Setup with reference projects
mcp-config setup mcp-workspace "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-workspace "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 Tools Py
• MCP Configuration Tool
• Cline MCP Servers Documentation
• Cline Extension for VSCode
• Model Context Protocol Documentation