Shemcp - the simple shell mcp server.

Independent agentic coding without handing over the keys to the castle. Stop getting approval prompts that are unimportant.

What's new

• Git Worktree Support: Automatically detects and allows access to git worktrees created from the sandbox repository. Worktrees are validated via git worktree list and added to an allowlist for the session. Disable with worktree_detection = false in the [security] section of your config file.

• 🆕 Pagination Support: Added pagination and large output handling to shell_exec with configurable limit_bytes, limit_lines, and on_large_output modes

• 🆕 Spill File Management: Large outputs are automatically written to temporary files with spill_uri for safe, paginated reading

• 🆕 New read_file_chunk Tool: Read paginated data from spilled files using cursor and limit_bytes for safe streaming

• Sandbox root now resolves to the Git repository root by default (fallback to the current working directory), with optional overrides via SHEMCP_ROOT or MCP_SANDBOX_ROOT.

• Removed the shell_set_cwd tool; shell_exec cwd can be relative to the sandbox root, or an absolute path within the sandbox or a valid git worktree.

• Added shell_info tool for introspection (reports sandbox_root and resolves relative cwd inputs, including within_sandbox checks).

• Hardened ensureCwd with realpath and boundary checks to prevent symlink escapes and ensure directory accessibility.

• Updated docs and tests to reflect the new behavior.

Related MCP server: MCP Shell Server

Overview

This MCP server provides sandboxed shell command execution with comprehensive security policies. It allows AI assistants to safely execute shell commands while enforcing strict access controls through configurable TOML files.

Sandbox root selection

To avoid the sandbox accidentally shrinking to a nested subdirectory, shemcp derives a stable sandbox root at startup using the following precedence:

1. SHEMCP_ROOT or MCP_SANDBOX_ROOT environment variable (if set and exists)

2. Nearest Git repository root discovered from the agent's process.cwd()

3. process.cwd() as a final fallback

The chosen root remains fixed for the duration of the process. Working directories for command execution can be relative paths inside this sandbox, or absolute paths within the sandbox or a valid git worktree.

• shell_exec optionally accepts a cwd that can be relative to the sandbox root, or an absolute path within the sandbox or a valid git worktree.

This ensures that if the client happens to start the agent several levels deep, the sandbox still resolves to the project root (typically the Git root), preventing the MCP from becoming unable to access sibling paths in the repository.

You can explicitly override the root for special cases with SHEMCP_ROOT or MCP_SANDBOX_ROOT.

Features

• 📋 TOML Configuration: Easy-to-edit configuration files with validation

• 🔒 Command Allowlisting: Only pre-approved commands can be executed

• 🚫 Command Denylisting: Explicitly block dangerous command patterns

• 📁 Sandboxed to Project Root: Commands run within the Git repository root by default (fallback to current working directory). Override with SHEMCP_ROOT or MCP_SANDBOX_ROOT.

• 🌿 Git Worktree Support: Automatically detects and allows access to git worktrees (sibling directories created via git worktree add)

• 🛡️ Hardened Path Enforcement: cwd can be relative or absolute within sandbox/worktree boundaries. Realpath boundary checks prevent symlink escapes.

• 🌍 Environment Filtering: Only pass through safe environment variables

• ⏱️ Resource Limits: Configurable timeouts and output size caps

• 📄 Pagination Support: Handle large command outputs with configurable limit_bytes and limit_lines

• 💾 Spill File Management: Large outputs automatically written to temporary files for safe, paginated access

• 🔄 Streaming Reads: read_file_chunk tool for reading spilled files in token-safe chunks

Security Model

The server implements multiple layers of security:

1. Command Validation: Commands must match allowlist patterns and not match denylist patterns

2. Directory Sandboxing: Commands can only run within the sandbox root (Git repository root by default; fallback to CWD) or valid git worktrees. cwd can be relative or absolute within these boundaries. Override root via SHEMCP_ROOT or MCP_SANDBOX_ROOT.

3. Environment Isolation: Sensitive environment variables are filtered out

4. Resource Limits: Prevent runaway processes with timeouts and output limits

Debugging

The server writes debug logs to ~/.shemcp/debug.log which can help diagnose issues:

# View the debug log
tail -f ~/.shemcp/debug.log

# Clear the debug log
> ~/.shemcp/debug.log

The log captures:

• Server startup and configuration loading

• All MCP requests received

• Shutdown signals and cleanup process

• Any errors or exceptions

Default Policy

• Allowed Commands: git, gh, make, grep, sed, jq, aws, az, bash -lc

• Denied Patterns: git push to main/master branches

• Root Directory: Git repository root by default (fallback to process.cwd()). Override via SHEMCP_ROOT or MCP_SANDBOX_ROOT.

• Timeout: 600 seconds per command

• Max Output: 2MB per stream (stdout/stderr)

Commands

1) shell_exec

Execute an allow-listed command inside the sandbox with support for pagination and large output handling.

Parameters:

• cmd (required): Command to run (e.g., "git", "npm", "python")

• args: Array of string arguments (e.g., ["status", "--short"])

• cwd: Optional working directory (relative to sandbox root, or absolute path within sandbox/worktree)

• timeout_ms: Command timeout in milliseconds (deprecated, use timeout_seconds)

• timeout_seconds: Command timeout in seconds (1-600, clamped to policy limits)

• max_output_bytes: Maximum output size in bytes (1000-10M, clamped to policy limits)

• page (required): Pagination configuration object:

  • cursor: Opaque position marker (e.g., "bytes:0")

  • limit_bytes: Maximum bytes per page (default: 40000, ~10k tokens)

  • limit_lines: Maximum lines per page (default: 2000, stops on whichever hits first)

• on_large_output: How to handle large outputs: "spill" (default), "truncate", or "error"

Rules:

• A page object must be supplied; otherwise the request is rejected with Error: pagination parameters are required

• cwd can be relative to sandbox root, or an absolute path within the sandbox or a valid git worktree

• Paths outside the sandbox/worktree boundaries are rejected with a clear error message

• Large outputs (>limit_bytes or >limit_lines) are handled according to on_large_output mode

Response Format:

{
  "exit_code": 0,
  "stdout_chunk": "first 40k of data...",
  "stderr_chunk": "",
  "bytes_start": 0,
  "bytes_end": 39999,
  "total_bytes": 58112234,
  "truncated": false,
  "next_cursor": "bytes:40000",
  "spill_uri": "mcp://tmp/exec-abc123.out",
  "mime": "text/plain",
  "line_count": 1780,
  "stderr_count": 0,
  "cmdline": ["git", "log"],
  "cwd": "/path/to/project",
  "limits": {
    "timeout_ms": 60000,
    "max_output_bytes": 2000000
  }
}

2) read_file_chunk

Read paginated data from a spilled file created by shell_exec when on_large_output is set to "spill".

Parameters:

• uri (required): URI of the spilled file (e.g., "mcp://tmp/exec-abc123.out")

• cursor: Opaque position marker (default: "bytes:0")

• limit_bytes: Maximum bytes to read (default: 40000)

Response Format:

{
  "data": "chunk of file content...",
  "bytes_start": 0,
  "bytes_end": 39999,
  "total_bytes": 58112234,
  "next_cursor": "bytes:40000",
  "mime": "text/plain"
}

3) shell_info

Introspection utility for the sandbox.

• Parameters (optional):

  • cwd: Relative path to resolve and validate against the sandbox root

• Returns: JSON including sandbox_root, and if cwd is provided, resolved_path and within_sandbox flags

4) Removed: shell_set_cwd

This command has been removed. Use shell_exec with a relative cwd instead.

Quick reference

Ask your MCP client to call these tools with the following inputs:

• shell_info examples:

  • { "cwd": "." } → returns sandbox_root, resolves to the root, and confirms within sandbox

  • { "cwd": "src" } → returns resolved src path and within_sandbox: true if it exists/inside

• shell_exec examples:

• { "cmd": "git", "args": ["status"], "cwd": ".", "page": { "cursor": { "cursor_type": "bytes", "offset": 0 } } }

• { "cmd": "npm", "args": ["test"], "cwd": ".", "page": { "cursor": { "cursor_type": "bytes", "offset": 0 } } }

• { "cmd": "ls", "args": ["-la"], "cwd": "src", "page": { "cursor": { "cursor_type": "bytes", "offset": 0 } } }

• Pagination examples:

  • { "cmd": "git", "args": ["log"], "page": { "cursor": { "cursor_type": "bytes", "offset": 0 }, "limit_bytes": 32768 } } → First 32KB of git log

  • { "cmd": "cat", "args": ["large.log"], "page": { "cursor": { "cursor_type": "bytes", "offset": 40000 } } } → Next page from byte 40000

  • { "cmd": "find", "args": [".", "-name", "*.ts"], "page": { "cursor": { "cursor_type": "bytes", "offset": 0 } }, "on_large_output": "spill" } → Spill large find results to file

• Spill file reading examples:

  • { "uri": "mcp://tmp/exec-abc123.out", "cursor": { "cursor_type": "bytes", "offset": 0 }, "limit_bytes": 16384 } → Read first 16KB of spilled file

  • { "uri": "mcp://tmp/exec-abc123.out", "cursor": { "cursor_type": "bytes", "offset": 16384 }, "limit_bytes": 16384 } → Read next 16KB chunk

Quick Start

1. Setup for Claude Code

Add the MCP server using Claude Code's CLI with npx (recommended):

# Add the shell MCP server to Claude Code (uses latest version)
claude mcp add shell -- npx -y shemcp@latest

# Verify it was added successfully
claude mcp list

Alternative scopes:

# Add for current project only (default)
claude mcp add shell -- npx -y shemcp@latest

# Add for current user (available in all projects)
claude mcp add --scope user shell -- npx -y shemcp@latest

# Add for project team (creates .mcp.json in project root)
claude mcp add --scope project shell -- npx -y shemcp@latest

2. Setup for Other MCP Clients

For Cursor/VS Code with MCP:

{
  "mcp.servers": {
    "shell": {
      "command": "npx",
      "args": ["-y", "shemcp@latest"],
      "env": {}
    }
  }
}

For Desktop MCP Clients:

• Command: npx

• Arguments: ["-y", "shemcp@latest"]

3. Optional: Custom Configuration

The server works out of the box with sensible defaults. If you need to customize the configuration:

# Create config directory
mkdir -p ~/.config/shemcp

# Download and customize the example config
curl -o ~/.config/shemcp/config.toml https://raw.githubusercontent.com/acartine/shemcp/main/config.example.toml

# Edit the config to match your needs
nano ~/.config/shemcp/config.toml

4. Alternative: Install Globally (Optional)

If you prefer to install shemcp globally instead of using npx:

# Global installation
npm install -g shemcp

# Then use direct command in MCP config
claude mcp add shell -- shemcp

For development from source:

git clone https://github.com/acartine/shemcp.git
cd shemcp
npm install
npm run build

# Add local version to Claude Code
claude mcp add shell -- node /absolute/path/to/shemcp/dist/index.js

Configuration

The server works with sensible built-in defaults. Configuration files are optional and only needed for customization.

If present, configuration is loaded from (in priority order):

1. ~/.config/shemcp/config.toml (user config - highest priority)

2. /etc/shemcp/config.toml (system config - lower priority)

3. Built-in defaults (always used as fallback)

Configuration Structure

# Configuration format version (not the package version)
config_version = 1

[server]
name = "shemcp"

[directories]
# The sandbox root defaults to the Git repository root (fallback to the current
# working directory) and remains fixed for the process lifetime.
# Override with SHEMCP_ROOT or MCP_SANDBOX_ROOT environment variables if needed.

[commands]
allow = ["^git(\\s|$)", "^npm(\\s|$)", "^make(\\s|$)"]
deny = ["^git\\s+push\\s+(origin\\s+)?(main|master)"]

[limits]
timeout_seconds = 600
max_output_bytes = 2000000

[environment]
whitelist = ["PATH", "HOME", "USER", "LANG"]

[security]
require_secure_permissions = false
worktree_detection = true  # Enable automatic git worktree detection

See config.example.toml for a complete example with documentation.

Example Usage

Once configured with Claude Code or another MCP client, you can ask the AI to execute shell commands:

Example interactions:

• "Check the git status of my project" → Executes git status

• "List all TypeScript files" → Executes find . -name "*.ts"

• "Run the tests" → Executes npm test

• "Show recent commits" → Executes git log --oneline -10

• "Create a new branch for this feature" → Executes git checkout -b feature-name

The AI can only execute commands that match your allow patterns and run in directories you've permitted, providing a secure sandbox for shell operations.

Pagination Usage Scenarios

Handling Large Command Outputs

When dealing with commands that produce large outputs (like logs, large files, or directory listings), use pagination to avoid token limits:

Scenario 1: Paginating through git log

{
  "cmd": "git",
  "args": ["log", "--oneline"],
  "page": { "cursor": { "cursor_type": "bytes", "offset": 0 }, "limit_bytes": 32768 }
}

Returns first 32KB of git history with next_cursor for continuation.

Scenario 2: Reading large files in chunks

{
  "cmd": "cat",
  "args": ["huge.log"],
  "on_large_output": "spill",
  "page": { "cursor": { "cursor_type": "bytes", "offset": 0 }, "limit_bytes": 40000 }
}

Spills large log file and returns first 40KB with spill_uri for continued reading.

Scenario 3: Processing large directory listings

{
  "cmd": "find",
  "args": [".", "-type", "f", "-name", "*.js"],
  "page": { "cursor": { "cursor_type": "bytes", "offset": 0 }, "limit_lines": 1000 }
}

Returns up to 1000 lines of file listing, whichever comes first.

Reading Spill Files

When shell_exec returns a spill_uri, use read_file_chunk to read the data in manageable chunks:

Scenario 4: Reading spilled output

{
  "uri": "mcp://tmp/exec-abc123.out",
  "cursor": { "cursor_type": "bytes", "offset": 0 },
  "limit_bytes": 16384
}

Reads first 16KB of the spilled file.

Scenario 5: Continuing to read spilled output

{
  "uri": "mcp://tmp/exec-abc123.out",
  "cursor": { "cursor_type": "bytes", "offset": 16384 },
  "limit_bytes": 16384
}

Reads the next 16KB chunk using the next_cursor from the previous response.

Agent Behavior Patterns

Automatic Pagination Loop:

// Pseudo-code for automatic pagination
let result = shell_exec(cmd, args, { page: { limit_bytes: 40000 } });
while (result.next_cursor) {
  // Process current chunk
  processChunk(result.stdout_chunk);

  // Get next chunk
  result = shell_exec(cmd, args, {
    page: { cursor: result.next_cursor }
  });
}

Spill File Handling:

// Pseudo-code for handling spilled files
let result = shell_exec(cmd, args, { on_large_output: "spill", page: {} });
if (result.spill_uri) {
  let chunk = read_file_chunk(result.spill_uri, 40000);
  while (chunk.next_cursor) {
    processChunk(chunk.data);
    chunk = read_file_chunk(result.spill_uri, chunk.next_cursor);
  }
}

Development

# Run tests
npm test

# Run tests with UI
npm test:ui

# Build TypeScript
npm run build

# Development mode
npm run dev

Git Worktree Support

shemcp automatically supports git worktrees, which are commonly used for parallel development workflows. When an agent creates a worktree (e.g., git worktree add ../repo-feature -b feature), the worktree is created as a sibling directory outside the primary sandbox.

How it works

1. When a path outside the sandbox is requested, shemcp checks if it matches the worktree naming pattern (sibling directory starting with the sandbox basename)

2. If it matches, shemcp runs git worktree list to verify it's a legitimate worktree

3. Verified worktrees are added to a session allowlist for efficient subsequent access

4. The worktree list is cached for 60 seconds to minimize git command overhead

Example

/Users/user/myproject           # Primary sandbox (git root)
/Users/user/myproject-feature   # Worktree - automatically allowed
/Users/user/myproject-bugfix    # Worktree - automatically allowed
/Users/user/other-project       # NOT allowed - different project

Disabling Worktree Detection

If you prefer stricter security and don't need worktree support, disable it in your config file:

# In ~/.config/shemcp/config.toml
[security]
worktree_detection = false

When disabled, only paths within the primary sandbox root are allowed.

Security Considerations

⚠️ Important Security Notes:

1. Configuration Security: Config files should not be world-writable. The server warns about insecure permissions.

2. No Project-Level Configs: By design, there are no .shemcp.toml files in working directories to prevent AI from modifying its own security constraints.

3. Principle of Least Privilege: Start with restrictive settings and gradually add permissions as needed.

4. Regular Auditing: Review your allowed commands and directories periodically.

Testing

The project includes a comprehensive test suite covering:

• Configuration loading and validation

• Policy enforcement

• Command allowlisting/denylisting

• Directory access controls

• Environment filtering

• Tool definitions

• Server configuration

Run tests with: npm test

Troubleshooting

Common Issues

"Command not allowed" errors:

• Check your commands.allow patterns in the config

• Ensure the command matches the regex patterns

• Verify the command isn't in the commands.deny list

"Directory not allowed" errors:

• The sandbox root is the Git project root (or process.cwd() if no Git repo). All paths must be inside it.

• Use SHEMCP_ROOT or MCP_SANDBOX_ROOT to override for special cases.

• Ensure the directory exists and is accessible.

Server not connecting:

• Verify you're using npx -y shemcp@latest in your MCP client config

• If using a local installation, check that the server was built with npm run build

• Look for error messages in the MCP client logs

• Check the debug log at ~/.shemcp/debug.log

Debug Configuration

To see your current configuration:

# List Claude Code MCP servers
claude mcp list

# Get details about your shell server
claude mcp get shell

# Remove server if needed
claude mcp remove shell

# Check which config files exist (optional - only if you created custom config)
ls -la ~/.config/shemcp/config.toml
ls -la /etc/shemcp/config.toml

License

MIT