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Server Configuration Guide

This guide helps you choose the right configuration for your use case and shows you how to apply it. For the complete reference of available toolsets and tools, see the README.

Quick Reference

We currently support the following ways in which the GitHub MCP Server can be configured:

Configuration Remote Server Local Server
Toolsets X-MCP-Toolsets header or /x/{toolset} URL --toolsets flag or GITHUB_TOOLSETS env var
Individual Tools X-MCP-Tools header --tools flag or GITHUB_TOOLS env var
Read-Only Mode X-MCP-Readonly header or /readonly URL --read-only flag or GITHUB_READ_ONLY env var
Dynamic Mode Not available --dynamic-toolsets flag or GITHUB_DYNAMIC_TOOLSETS env var
Lockdown Mode X-MCP-Lockdown header --lockdown-mode flag or GITHUB_LOCKDOWN_MODE env var

Default behavior: If you don't specify any configuration, the server uses the default toolsets: context, issues, pull_requests, repos, users.

How Configuration Works

All configuration options are composable: you can combine toolsets, individual tools, dynamic discovery, read-only mode and lockdown mode in any way that suits your workflow.

Note: read-only mode acts as a strict security filter that takes precedence over any other configuration, by disabling write tools even when explicitly requested.

Configuration Examples

The examples below use VS Code configuration format to illustrate the concepts. If you're using a different MCP host (Cursor, Claude Desktop, JetBrains, etc.), your configuration might need to look slightly different. See installation guides for host-specific setup.

Enabling Specific Tools

Best for: users who know exactly what they need and want to optimize context usage by loading only the tools they will use.

Example:

Remote ServerLocal Server
{
  "type": "http",
  "url": "https://api.githubcopilot.com/mcp/",
  "headers": {
    "X-MCP-Tools": "get_file_contents,get_me,pull_request_read"
  }
}
 
{
  "type": "stdio",
  "command": "go",
  "args": [
    "run",
    "./cmd/github-mcp-server",
    "stdio",
    "--tools=get_file_contents,get_me,pull_request_read"
  ],
  "env": {
    "GITHUB_PERSONAL_ACCESS_TOKEN": "${input:github_token}"
  }
}

Enabling Specific Toolsets

Best for: Users who want to enable multiple related toolsets.

Remote ServerLocal Server
{
  "type": "http",
  "url": "https://api.githubcopilot.com/mcp/",
  "headers": {
    "X-MCP-Toolsets": "issues,pull_requests"
  }
}
 
{
  "type": "stdio",
  "command": "go",
  "args": [
    "run",
    "./cmd/github-mcp-server",
    "stdio",
    "--toolsets=issues,pull_requests"
  ],
  "env": {
    "GITHUB_PERSONAL_ACCESS_TOKEN": "${input:github_token}"
  }
}

Enabling Toolsets + Tools

Best for: Users who want broad functionality from some areas, plus specific tools from others.

Enable entire toolsets, then add individual tools from toolsets you don't want fully enabled.

Remote ServerLocal Server
{
  "type": "http",
  "url": "https://api.githubcopilot.com/mcp/",
  "headers": {
    "X-MCP-Toolsets": "repos,issues",
    "X-MCP-Tools": "get_gist,pull_request_read"
  }
}
 
{
  "type": "stdio",
  "command": "go",
  "args": [
    "run",
    "./cmd/github-mcp-server",
    "stdio",
    "--toolsets=repos,issues",
    "--tools=get_gist,pull_request_read"
  ],
  "env": {
    "GITHUB_PERSONAL_ACCESS_TOKEN": "${input:github_token}"
  }
}

Result: All repository and issue tools, plus just the gist tools you need.

Read-Only Mode

Best for: Security conscious users who want to ensure the server won't allow operations that modify issues, pull requests, repositories etc.

When active, this mode will disable all tools that are not read-only even if they were requested.

Example:

Remote ServerLocal Server

Option A: Header

{
  "type": "http",
  "url": "https://api.githubcopilot.com/mcp/",
  "headers": {
    "X-MCP-Toolsets": "issues,repos,pull_requests",
    "X-MCP-Readonly": "true"
  }
}

Option B: URL path

{
  "type": "http",
  "url": "https://api.githubcopilot.com/mcp/x/all/readonly"
}
 
{
  "type": "stdio",
  "command": "go",
  "args": [
    "run",
    "./cmd/github-mcp-server",
    "stdio",
    "--toolsets=issues,repos,pull_requests",
    "--read-only"
  ],
  "env": {
    "GITHUB_PERSONAL_ACCESS_TOKEN": "${input:github_token}"
  }
}

Even if issues toolset contains create_issue, it will be excluded in read-only mode.

Dynamic Discovery (Local Only)

Best for: Letting the LLM discover and enable toolsets as needed.

Starts with only discovery tools (enable_toolset, list_available_toolsets, get_toolset_tools), then expands on demand.

Local Server Only
{
  "type": "stdio",
  "command": "go",
  "args": [
    "run",
    "./cmd/github-mcp-server",
    "stdio",
    "--dynamic-toolsets"
  ],
  "env": {
    "GITHUB_PERSONAL_ACCESS_TOKEN": "${input:github_token}"
  }
}

With some tools pre-enabled:

{
  "type": "stdio",
  "command": "go",
  "args": [
    "run",
    "./cmd/github-mcp-server",
    "stdio",
    "--dynamic-toolsets",
    "--tools=get_me,search_code"
  ],
  "env": {
    "GITHUB_PERSONAL_ACCESS_TOKEN": "${input:github_token}"
  }
}

When both dynamic mode and specific tools are enabled in the server configuration, the server will start with the 3 dynamic tools + the specified tools.

Lockdown Mode

Best for: Public repositories where you want to limit content from users without push access.

Lockdown mode ensures the server only surfaces content in public repositories from users with push access to that repository. Private repositories are unaffected, and collaborators retain full access to their own content.

Example:

Remote ServerLocal Server
{
  "type": "http",
  "url": "https://api.githubcopilot.com/mcp/",
  "headers": {
    "X-MCP-Lockdown": "true"
  }
}
 
{
  "type": "stdio",
  "command": "go",
  "args": [
    "run",
    "./cmd/github-mcp-server",
    "stdio",
    "--lockdown-mode"
  ],
  "env": {
    "GITHUB_PERSONAL_ACCESS_TOKEN": "${input:github_token}"
  }
}

Troubleshooting

Problem Cause Solution
Server fails to start Invalid tool name in --tools or X-MCP-Tools Check tool name spelling; use exact names from Tools list
Write tools not working Read-only mode enabled Remove --read-only flag or X-MCP-Readonly header
Tools missing Toolset not enabled Add the required toolset or specific tool
Dynamic tools not available Using remote server Dynamic mode is available in the local MCP server only

Useful links