MCP Directory

How to add CLI MCP Server to Claude Desktop

Securely run whitelisted CLI commands within an allowed directory via MCP. Paste the config into ~/Library/Application Support/Claude/claude_desktop_config.json and restart Claude Desktop.

Last updated June 14, 2026 · 171★ · stdio · no auth

Claude Desktop config for CLI MCP Server

npx @smithery/cli install cli-mcp-server --client claude
{
  "mcpServers": {
    "cli-mcp-server": {
      "command": "uvx",
      "args": [
        "cli-mcp-server"
      ],
      "env": {
        "ALLOWED_DIR": "</your/desired/dir>",
        "ALLOWED_COMMANDS": "ls,cat,pwd,echo",
        "ALLOWED_FLAGS": "-l,-a,--help,--version",
        "MAX_COMMAND_LENGTH": "1024",
        "COMMAND_TIMEOUT": "30",
        "ALLOW_SHELL_OPERATORS": "false"
      }
    }
  }
}

Requires `uv` (the Python package runner). Install it from https://docs.astral.sh/uv/ if `uvx` is not found.

Setup steps

  1. 1Open Claude Desktop → Settings → Developer → Edit Config (this opens ~/Library/Application Support/Claude/claude_desktop_config.json).
  2. 2Paste the CLI MCP Server config below under the top-level "mcpServers" key.
  3. 3Fill in any placeholder secrets (API keys, paths) in the snippet.
  4. 4Save the file, then fully quit and reopen Claude Desktop.
  5. 5Open a chat and confirm CLI MCP Server's tools appear under the 🔌 tools menu.

Before you start

  • Python 3.10+
  • MCP protocol library
  • uv / uvx (for running the server)

What CLI MCP Server can do in Claude Desktop

run_command

Executes whitelisted CLI commands within allowed directories. Takes a single command string (e.g., 'ls -l' or 'cat file.txt'). Shell operators are not supported unless ALLOW_SHELL_OPERATORS=true; commands and flags must be whitelisted unless set to 'all'; all paths are validated to be within ALLOWED_DIR.

show_security_rules

Displays the current security configuration and restrictions, including the working directory, allowed commands, allowed flags, and security limits (max command length and timeout).

Security

Shell operators (&&, |, >, >>) are blocked by default but can be enabled with ALLOW_SHELL_OPERATORS=true. Commands must be whitelisted unless ALLOWED_COMMANDS='all'; flags must be whitelisted unless ALLOWED_FLAGS='all'. Setting either to 'all' removes that restriction entirely. All paths are validated and normalized to be within ALLOWED_DIR, with path-traversal prevention and symlink resolution. Execution is bounded by MAX_COMMAND_LENGTH and COMMAND_TIMEOUT.

CLI MCP Server + Claude Desktop FAQ

Where is the Claude Desktop config file?

Claude Desktop reads MCP servers from ~/Library/Application Support/Claude/claude_desktop_config.json. Paste the CLI MCP Server config there under the "mcpServers" key and restart the client.

Is CLI MCP Server safe to use with Claude Desktop?

Shell operators (&&, |, >, >>) are blocked by default but can be enabled with ALLOW_SHELL_OPERATORS=true. Commands must be whitelisted unless ALLOWED_COMMANDS='all'; flags must be whitelisted unless ALLOWED_FLAGS='all'. Setting either to 'all' removes that restriction entirely. All paths are validated and normalized to be within ALLOWED_DIR, with path-traversal prevention and symlink resolution. Execution is bounded by MAX_COMMAND_LENGTH and COMMAND_TIMEOUT.

How do I allow any command or flag?

Set ALLOWED_COMMANDS or ALLOWED_FLAGS to 'all'. This removes the respective whitelist restriction; otherwise only the comma-separated listed values are permitted.

Why are shell operators like && and | not working?

Shell operators (&&, ||, |, >, >>) are blocked by default to prevent injection. Enable them by setting ALLOW_SHELL_OPERATORS=true.

What configuration is required?

ALLOWED_DIR is required and has no default; it sets the base directory for command execution. All other variables (ALLOWED_COMMANDS, ALLOWED_FLAGS, MAX_COMMAND_LENGTH, COMMAND_TIMEOUT, ALLOW_SHELL_OPERATORS) have defaults.

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