MCP Command Server

A Model Context Protocol (MCP) server that enables secure command execution on the host system. This server allows AI assistants like Claude to run shell commands with optional working directory and stdin support.

The project is now modularized to support multiple transport methods: stdio, HTTP, and Server-Sent Events (SSE).

Features

• Command Execution: Run any shell command on the host system
• Working Directory Support: Execute commands in specific directories
• STDIN Support: Pipe input data to commands
• Cross-Platform: Works on macOS, Linux, and Windows
• Timeout Protection: Commands timeout after 60 seconds to prevent hanging
• Special Fish Shell Support: Enhanced handling for the Fish shell
• Advanced Logging: Powered by Logback with configurable log levels (ERROR, WARN, INFO, DEBUG, TRACE), optional file logging, and rolling file support

Prerequisites

• Java 25 or higher
• Gradle (for building from source)
• Claude Desktop app (for integration)

Installation

Building from Source

1. Clone the repository:

git clone <repository-url>
cd mcp-server-command

2. Build the project:

./gradlew build

This will create JAR files for each module:

• stdio/build/libs/stdio-1.0.0.jar - Standard I/O transport (recommended for Claude Desktop)
• http/build/libs/http-1.0.0.jar - HTTP transport
• sse/build/libs/sse-1.0.0.jar - Server-Sent Events transport

Native Binary (Optional)

For better performance, you can build a native binary using GraalVM:

./gradlew stdio:nativeCompile

This creates a native executable at stdio/build/native/nativeCompile/mcp-server-command

Pre-built JAR

If you have a pre-built JAR, skip the building step and proceed to configuration.

Configuration

Claude Desktop Integration

1. Locate your Claude Desktop configuration:

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

2. Add the MCP server configuration:

Option A: Java JAR (Recommended)

{
  "mcpServers": {
    "mcp-server-command": {
      "command": "java",
      "args": [
        "-jar",
        "/absolute/path/to/stdio-1.0.0.jar"
      ],
      "env":{
        "LOG_DIR":"/Users/<username>/Library/Logs/Claude",
        "LOG_LEVEL":"DEBUG"
      }
    }
  }
}

Option B: Native Binary

{
  "mcpServers": {
    "mcp-server-command": {
      "command": "/absolute/path/to/stdio/build/native/nativeCompile/mcp-server-command",
      "env":{
        "LOG_DIR":"/Users/<username>/Library/Logs/Claude",
        "LOG_LEVEL":"DEBUG"
      }
    }
  }
}

3. Restart Claude Desktop to load the new server

Usage

Once configured, Claude can use the run_command tool to execute commands on your system.

Basic Examples

Simple command execution:

Run the command: ls -la

Command with working directory:

Run 'git status' in the directory /Users/username/my-project

Command with stdin:

Create a new file called hello.txt with the content "Hello, World!" using the cat command

Python script execution:

Run this Python script:
print("Hello from Python")
for i in range(5):
    print(f"Count: {i}")

API Reference

Tool: run_command

Executes a command on the host system.

Parameters:

• command (string, required): The command to execute with arguments
• workdir (string, optional): The working directory for command execution
• stdin (string, optional): Text to pipe into the command's STDIN

Returns:

• stdout: Standard output from the command
• stderr: Standard error output from the command
• message: Error message if command fails
• isError: Boolean indicating if the command failed

Example Request:

{
  "jsonrpc": "2.0",
  "method": "tools/call",
  "id": 1,
  "params": {
    "name": "run_command",
    "arguments": {
      "command": "echo Hello World",
      "workdir": "/tmp",
      "stdin": "Input data"
    }
  }
}

Development

Project Structure

mcp-server-command/
├── stdio/                      # Standard I/O transport module
│   ├── src/main/java/com/brunorozendo/mcp/
│   │   └── McpServer.java      # Main server entry point
│   └── build.gradle
├── http/                       # HTTP transport module  
│   ├── src/main/java/com/brunorozendo/mcp/
│   │   └── McpServer.java      # HTTP server implementation
│   └── build.gradle
├── sse/                        # Server-Sent Events transport module
│   ├── src/main/java/com/brunorozendo/mcp/
│   │   └── McpServer.java      # SSE server implementation  
│   └── build.gradle
├── tools/                      # Shared command execution logic
│   ├── src/main/java/com/brunorozendo/mcp/
│   │   ├── CommandExecutor.java     # Command execution logic
│   │   ├── CommandResult.java       # Result data structure
│   │   ├── ExecCommandTool.java     # Tool implementation
│   │   ├── Transport.java           # Transport configuration
│   │   └── ToolSchemas.java         # Tool schema definitions
│   └── build.gradle
├── settings.gradle             # Multi-module configuration
└── docs/                       # Documentation

Running Tests

Execute the test script to verify functionality:

./test_server.sh

Building a Distribution

Create distribution archives (ZIP and TAR):

./gradlew distZip distTar

Security Considerations

⚠️ WARNING: This server executes commands with the same privileges as the user running the Java process.

Security Best Practices:

1. Only install this server if you trust the AI assistant
2. Run the server with minimal necessary privileges
3. Consider using a restricted user account for the server
4. Be cautious when sharing your screen or command outputs
5. Regularly review which commands are being executed
6. Consider implementing command whitelisting for production use

Potential Risks:

• File system access and modification
• Network operations
• Process execution
• Access to environment variables and system information

Troubleshooting

Server not appearing in Claude

1. Verify the configuration file path is correct
2. Ensure the JAR file path is absolute, not relative
3. Check that Java 25+ is installed: java -version
4. Restart Claude Desktop after configuration changes

Commands failing

1. Set log level to DEBUG or TRACE to see detailed error messages
2. Check file permissions for the working directory
3. Verify the command syntax is correct for your shell
4. Test commands directly in terminal first

Timeout errors

• Commands timeout after 60 seconds
• For long-running commands, consider breaking them into smaller steps
• Use background processes with caution

Advanced Usage

Creating Files

# Using cat with stdin
echo "File content" | cat > newfile.txt

# Or directly with stdin parameter
cat > newfile.txt
# with stdin: "File content"

Running Scripts

# Python
python3 -c "print('Hello')"

# Or with stdin for longer scripts
python3
# with stdin: <your script content>

Fish Shell Support

The server includes special handling for Fish shell to properly handle stdin:

fish -c "echo $USER"

Version History

• 1.0.0 - Current version with modular architecture
  • Modular design with stdio, HTTP, and SSE transport support
  • Command execution with timeout protection
  • Working directory support
  • STDIN support
  • Special Fish shell handling
  • Advanced Logback-based logging with file rotation support
  • Updated to MCP SDK 0.17.0
  • Java 25 support
  • GraalVM native compilation support

Custom Logback Configuration

For advanced users, you can provide your own logback.xml configuration file:

1. Create your custom logback.xml
2. Place it in the classpath or specify its location with -Dlogback.configurationFile=/path/to/logback.xml

License

[Add your license information here]

Contributing

[Add contribution guidelines if applicable]

Support

For issues and questions:

• Check the troubleshooting section
• Set appropriate log level for debugging
• [Add support contact/repository issues link]