Fathom MCP

A Model Context Protocol server that provides AI assistants with direct access to local document collections through file-first search capabilities.

Features

Search Capabilities

• Full-text search with boolean operators (AND, OR, NOT) and exact phrase matching
• Parallel search across multiple queries for faster results
• Fuzzy matching and context-aware result highlighting
• Powered by ugrep - No database or RAG infrastructure required

Organization

• Hierarchical collections - Organize knowledge using folder structures
• Scope control - Search globally, within collections, or in specific documents
• Smart discovery - Find documents by name or path patterns

Format Support

• Multiple document formats - PDF, DOCX, HTML, JSON, XML, and more
• Automatic format detection - No manual configuration required
• Smart filter integration - Uses pandoc, jq, and other tools
• Graceful degradation - Formats auto-disabled if tools unavailable
• See docs/supported-formats.md for full details

Security

• Read-only access - Server never modifies your documents
• Path validation - Prevents directory traversal attacks
• Command sandboxing - Filter commands run in restricted mode
• Whitelist enforcement - Shell filters validated before execution

Installation

From PyPI (Recommended)

Install Fathom MCP directly from PyPI:

pip install fathom-mcp

Or with uv:

uv pip install fathom-mcp

System Dependencies

This server requires the following system utilities:

# Ubuntu/Debian
sudo apt install ugrep poppler-utils

# macOS
brew install ugrep poppler

Supported Formats

Fathom MCP supports searching and reading multiple document formats:

Default Formats (No Additional Tools Required)

• Markdown (.md, .markdown)
• Plain Text (.txt, .rst)
• CSV (.csv)
• PDF (.pdf) - requires pdftotext (from poppler-utils)

Optional Formats (Requires External Tools)

• Microsoft Word (.doc, .docx) - requires pandoc or antiword
• OpenDocument (.odt) - requires pandoc
• EPUB (.epub) - requires pandoc
• HTML (.html, .htm) - requires pandoc
• RTF (.rtf) - requires pandoc
• JSON (.json) - requires jq
• XML (.xml) - requires pandoc

Quick Setup for Optional Formats

To enable all optional formats:

# macOS
brew install pandoc jq

# Linux (Ubuntu/Debian)
sudo apt install pandoc jq

# Windows (Chocolatey)
choco install pandoc jq

See docs/supported-formats.md for detailed installation instructions, configuration options, and troubleshooting.

Collections and Scope

The File Knowledge server organizes documents using a collection-based hierarchy that maps directly to your filesystem structure.

Understanding Collections

• A collection is simply a folder within your knowledge base root
• Collections can be nested to any depth
• Each document belongs to exactly one collection (its containing folder)
• The root directory itself is the top-level collection

Configuring the Knowledge Root

The knowledge root can be specified via:

Command-line argument (recommended for static setups):

fathom-mcp --root /path/to/documents

Configuration file:

knowledge:
  root: "/path/to/documents"

Environment variable:

export FMCP_KNOWLEDGE__ROOT=/path/to/documents

Search Scopes

All search operations support three scope levels:

• Global scope - Search across all documents in the knowledge base
• Collection scope - Limit search to a specific folder and its subfolders
• Document scope - Search within a single document only

This hierarchical approach enables efficient knowledge organization without requiring database infrastructure.

Configuration

Basic Configuration

Create a config.yaml with your settings:

knowledge:
  root: "./documents"

search:
  context_lines: 5        # Lines of context around matches
  max_results: 50         # Maximum results per search
  timeout: 30             # Search timeout in seconds

security:
  enable_shell_filters: true
  filter_mode: whitelist  # Recommended for production

exclude:
  patterns:
    - ".git/*"
    - "*.draft.*"
    - "*.tmp"

See config.example.yaml for all available options.

Environment Variables

All configuration options can be overridden using environment variables with the FMCP_ prefix:

export FMCP_KNOWLEDGE__ROOT=/path/to/documents
export FMCP_SEARCH__MAX_RESULTS=100
export FMCP_SECURITY__FILTER_MODE=whitelist

Use double underscores (__) to denote nested configuration levels.

API

Tools

The server implements six MCP tools organized into three categories:

Browse Operations

• list_collections - List folders and documents in a collection
• find_document - Find documents by name or path pattern

Search Operations

• search_documents - Full-text search with boolean operators
• search_multiple - Execute multiple searches in parallel

Read Operations

• read_document - Read document content with optional page selection
• get_document_info - Get document metadata and table of contents

list_collections

Browse the hierarchical structure of your knowledge base.

Arguments:

• path (string, optional): Collection path relative to root. Defaults to root level.

Returns:

• List of subcollections (folders)
• List of documents with their paths and formats

Example:

{
  "path": "programming/python"
}

find_document

Locate documents by filename or path pattern using fuzzy matching.

Arguments:

• query (string, required): Search term for document names
• limit (number, optional): Maximum results to return (default: 20)

Returns:

• List of matching documents with paths and relevance scores

Example:

{
  "query": "async patterns",
  "limit": 10
}

search_documents

Execute full-text searches across your knowledge base with powerful boolean operators.

Arguments:

• query (string, required): Search query with optional operators
• scope (object, required): Defines search boundaries
  • type (string): One of "global", "collection", or "document"
  • path (string, conditional): Required for collection and document scopes

Search Operators:

• term1 term2 - AND: Find documents containing both terms
• term1|term2 - OR: Find documents containing either term
• term1 -term2 - NOT: Exclude documents with term2
• "exact phrase" - Match exact phrase with quotes

Returns:

• List of matches with document path, line numbers, and context
• Truncation indicator if results exceed maximum

Examples:

Global search:

{
  "query": "authentication jwt",
  "scope": {
    "type": "global"
  }
}

Collection-scoped search:

{
  "query": "async|await -deprecated",
  "scope": {
    "type": "collection",
    "path": "programming/python"
  }
}

Document-specific search:

{
  "query": "\"error handling\"",
  "scope": {
    "type": "document",
    "path": "guides/best-practices.md"
  }
}

search_multiple

Execute multiple search queries concurrently for improved performance.

Arguments:

• queries (array of strings, required): List of search queries
• scope (object, required): Same scope structure as search_documents

Returns:

• Object mapping each query to its search results
• Each result includes matches and truncation status

Example:

{
  "queries": ["authentication", "authorization", "session management"],
  "scope": {
    "type": "collection",
    "path": "security/docs"
  }
}

Note: Concurrent searches are limited by the limits.max_concurrent_searches configuration setting.

read_document

Read the complete contents of a document with optional page selection for PDFs.

Arguments:

• path (string, required): Document path relative to knowledge root
• pages (array of numbers, optional): Specific pages to read (PDF only)

Returns:

• Document content as text
• Format metadata

Examples:

Read entire document:

{
  "path": "guides/user-manual.pdf"
}

Read specific pages:

{
  "path": "guides/user-manual.pdf",
  "pages": [1, 5, 10]
}

Note: Content length is limited by the limits.max_read_chars configuration setting.

get_document_info

Retrieve metadata and structural information about a document.

Arguments:

• path (string, required): Document path relative to knowledge root

Returns:

• File size and format
• Page count (for PDFs)
• Table of contents with page numbers (when available)
• Last modified timestamp

Example:

{
  "path": "reference/api-documentation.pdf"
}

Usage with Claude Desktop

Using Command-Line Arguments

Add this to your claude_desktop_config.json:

{
  "mcpServers": {
    "fathom-mcp": {
      "command": "fathom-mcp",
      "args": ["--root", "/path/to/your/documents"]
    }
  }
}

Using Configuration File

For more complex setups, use a configuration file:

{
  "mcpServers": {
    "fathom-mcp": {
      "command": "fathom-mcp",
      "args": ["--config", "/path/to/config.yaml"]
    }
  }
}

Using uv (Development)

When developing or running from source:

{
  "mcpServers": {
    "fathom-mcp": {
      "command": "uv",
      "args": [
        "--directory",
        "/path/to/fathom-mcp",
        "run",
        "fathom-mcp",
        "--root",
        "/path/to/documents"
      ]
    }
  }
}

Configuration File Location

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

Important: Restart Claude Desktop after modifying the configuration file.

HTTP Transport Support

Fathom MCP supports two transport protocols for different deployment scenarios:

1. Stdio Transport (Default)

For Claude Desktop integration - the server communicates over standard input/output:

{
  "mcpServers": {
    "fathom-mcp": {
      "command": "fathom-mcp",
      "args": ["--root", "/path/to/your/documents"]
    }
  }
}

Docker (optional):

# Run stdio transport in Docker
docker compose --profile stdio up

2. HTTP Transport (Docker)

For remote deployment and web clients - the server runs as an HTTP service.

Streamable HTTP:

# Start server
docker compose --profile http up fathom-mcp-http

# Test connectivity
fathom-mcp-test -t streamable-http -u http://localhost:8765/mcp -l basic

Configuration

HTTP transport configured via environment variables or config file:

Environment variables:

export FMCP_TRANSPORT__TYPE=streamable-http
export FMCP_TRANSPORT__HOST=0.0.0.0
export FMCP_TRANSPORT__PORT=8765
export FMCP_TRANSPORT__ENABLE_CORS=true
export FMCP_TRANSPORT__ALLOWED_ORIGINS='["https://app.example.com"]'

Configuration file:

transport:
  type: "streamable-http"
  host: "0.0.0.0"
  port: 8765
  enable_cors: true
  allowed_origins:
    - "https://app.example.com"
  structured_logging: true

Security

⚠️ IMPORTANT: No Built-In Authentication

Fathom MCP does NOT include authentication for HTTP transport. This is intentional - authentication should be handled by dedicated tools.

For HTTP deployments:

• ✅ Use reverse proxy (Nginx, Caddy, Traefik) with authentication
• ✅ Use VPN (Tailscale, WireGuard) for network isolation
• ✅ Use HTTPS in production (never HTTP)
• ❌ Never expose HTTP transport directly to the internet
• ❌ Never use wildcard CORS (*) in production

For local use: Use the default stdio transport - no network access, no authentication needed.

See docs/security.md for detailed security setup with examples for reverse proxy, VPN, and OAuth.

Testing

Test client available for all transports:

# Connectivity test
fathom-mcp-test -t streamable-http -u http://localhost:8765/mcp -l connectivity

# Basic test suite
fathom-mcp-test -t streamable-http -u http://localhost:8765/mcp -l basic

# Full test suite with verbose output
fathom-mcp-test -t streamable-http -u http://localhost:8765/mcp -l full -v

Exit codes:

• 0: All tests passed
• 1: Some tests failed
• 2: Fatal error (cannot connect)
• 3: Configuration error
• 4: Timeout error
• 6: Partial success (connectivity OK, tools failed)

Docker Deployment

Using docker-compose (Recommended)

# Start the server
docker-compose up

# Build and start
docker-compose up --build

# Run in detached mode
docker-compose up -d

The included docker-compose.yaml provides:

• Read-only document mounting for security
• Resource limits (512MB memory, 1 CPU)
• Proper stdio configuration for MCP protocol

Manual Docker Build

# Build image
docker build -t fathom-mcp .

# Run with read-only mount
docker run -v /path/to/docs:/knowledge:ro fathom-mcp

# Run with custom configuration
docker run \
  -v /path/to/docs:/knowledge:ro \
  -v /path/to/config.yaml:/config/config.yaml:ro \
  fathom-mcp

Cloud Storage Integration

The File Knowledge server operates on local documents only. Cloud synchronization is intentionally handled outside the MCP server for security and architectural clarity.

Recommended Approaches

Option 1: Cloud Desktop Clients

• Google Drive Desktop, Dropbox, OneDrive, iCloud Drive
• Automatic background sync to local folder
• Point server to synced directory

Option 2: rclone mount

# Mount cloud storage as read-only local directory
rclone mount gdrive:Knowledge /data/knowledge --read-only --vfs-cache-mode full --daemon

Option 3: Scheduled sync

# Periodic sync via cron
*/30 * * * * rclone sync gdrive:Knowledge /data/knowledge

See docs/cloud-sync-guide.md for detailed setup instructions.

Development

Project Setup

# Clone repository
git clone https://github.com/RomanShnurov/fathom-mcp
cd fathom-mcp

# Install with development dependencies (recommended)
uv sync --extra dev

# Alternative: pip
pip install -e ".[dev]"

Running Tests

# Run all tests
uv run pytest

# Run with coverage report
uv run pytest --cov

# Run specific test file
uv run pytest tests/test_search.py

# Run with verbose output
uv run pytest -v

Code Quality Tools

# Format code
uv run ruff format .

# Lint code
uv run ruff check .

# Auto-fix linting issues
uv run ruff check . --fix

# Type checking
uv run mypy src

Security

The File Knowledge server implements defense-in-depth security.

Transport Security

⚠️ HTTP Transport Security: When using HTTP transport (streamable-http), the server does NOT include built-in authentication. This is intentional - use external tools:

• Reverse proxy (Nginx, Caddy, Traefik) with basic auth or OAuth
• VPN (Tailscale, WireGuard) for network isolation
• localhost only (host: 127.0.0.1) for same-machine access
• stdio transport (default) for local AI agents like Claude Desktop

📖 See docs/security.md for complete setup guides with configuration examples.

Path Security

• Path validation: All file paths validated against knowledge root
• Traversal prevention: Blocks ../ and absolute path attacks
• Symlink policy: Configurable symlink following (default: disabled)

Command Security

• Whitelist enforcement: Filter commands validated before execution
• Sandboxed execution: Shell commands run with timeout limits
• Read-only design: Server never modifies document collection
• No credential access: Server never touches cloud storage APIs

Configuration

security:
  enable_shell_filters: true
  filter_mode: whitelist          # Recommended for production
  allowed_filter_commands:
    - "pdftotext % -"
  symlink_policy: disallow        # Prevent symlink attacks

For production HTTP deployments, always use reverse proxy or VPN. See docs/security.md.

Debugging

Since MCP servers run over stdio, debugging can be challenging. Fathom MCP provides two options for interactive testing.

Built-in MCP Inspector (Recommended)

Fathom MCP includes a Streamlit-based inspector UI for testing server tools, resources, and prompts:

# Install inspector dependencies
uv sync --extra inspector

# Run the inspector
streamlit run inspector/app.py

The built-in Inspector provides:

• Interactive tool testing with dynamic forms
• Resource browsing and content reading
• Prompt listing and inspection
• Real-time server logs with filtering
• No external dependencies (Node.js not required)

External MCP Inspector

Alternatively, use the official MCP Inspector:

npx @modelcontextprotocol/inspector fathom-mcp --root /path/to/documents

You can also use it with configuration files:

npx @modelcontextprotocol/inspector fathom-mcp --config config.yaml

Contributing

Contributions are welcome! Please:

1. Fork the repository
2. Create a feature branch
3. Make your changes with tests
4. Run code quality checks (ruff format, ruff check, mypy)
5. Submit a pull request

See CONTRIBUTING.md for detailed guidelines.

License

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

Resources

Documentation

• Security Guide - Reverse proxy, VPN, and OAuth setup
• Supported Formats - Document format configuration
• Cloud Sync Guide - Cloud storage integration
• Integration Guide - Client setup and deployment
• Configuration Reference - All configuration options
• Tools Reference - Complete MCP tools documentation

External Resources

• Model Context Protocol - Official MCP documentation
• MCP Specification - Protocol specification
• ugrep - Ultra-fast grep with boolean search
• poppler-utils - PDF rendering utilities