GitHub Copilot CLI MCP Configuration Management Skill

GitHub Copilot CLI MCP Configuration Management

Configure MCP servers for GitHub Copilot CLI using the mcp-config.json file, which uses different syntax from VS Code's mcp.json.

Configuration Location

Default: ~/.copilot/mcp-config.json

Relocating the config directory (precedence, highest first):

--config-dir CLI flag: copilot --config-dir /path/to/dir
COPILOT_HOME environment variable: export COPILOT_HOME=/path/to/dir
Default ~/.copilot/

Setting either option redirects the entire config tree (agents, skills, MCP config, logs, sessions).

Project-level MCP configs: .mcp.json, .github/mcp.json, or .vscode/mcp.json — these take precedence over user-level definitions when server names conflict and are shared via source control.

Additional config at runtime: --additional-mcp-config augments ~/.copilot/mcp-config.json for the current session only. It is repeatable, and accepts either a JSON string or a file path prefixed with @:

copilot --additional-mcp-config '{"mcpServers":{"extra":{"type":"stdio","command":"npx","args":["my-server"],"tools":["*"]}}}' \
        --additional-mcp-config @/path/to/project-mcp.json

CLI Commands

Management Commands

These are slash commands entered inside the Copilot CLI interactive session (not shell commands):

/mcp add                  # Interactive form — Tab to navigate fields, Ctrl+S to save
/mcp show                 # List all configured servers
/mcp show SERVER-NAME     # Details for a specific server
/mcp edit SERVER-NAME     # Edit an existing server
/mcp delete SERVER-NAME   # Delete a server
/mcp disable SERVER-NAME  # Disable a server (keeps config, stops loading)
/mcp enable SERVER-NAME   # Re-enable a disabled server

Note: /mcp add is fully interactive — no server name argument is passed. Start Copilot CLI with copilot, then type /mcp add at the prompt.

Configuration Syntax

Root Structure

GitHub Copilot CLI uses mcpServers (VS Code uses servers):

{
  "mcpServers": {
    "server-name": { /* config */ }
  }
}

Server Types

GitHub Copilot CLI supports four server types:

Types: `stdio` / `local` (Subprocess — standard transport)

stdio and local are equivalent: both launch a subprocess and communicate via stdin/stdout. stdio is the portable standard name (aligns with VS Code, the Copilot cloud agent, and the MCP spec); local is a CLI-specific alias that also works.

{
  "mcpServers": {
    "azure": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@azure/mcp@latest", "server", "start"],
      "tools": ["*"],
      "env": {}
    },
    "serena": {
      "type": "local",
      "command": "uvx",
      "args": ["--from", "git+https://github.com/oraios/serena", "serena", "start-mcp-server"],
      "tools": ["*"],
      "env": {
        "API_KEY": "${MY_API_KEY}"
      }
    }
  }
}

Type: `http` (HTTP Server)

Connect to HTTP-based MCP server:

{
  "mcpServers": {
    "github": {
      "type": "http",
      "url": "https://api.githubcopilot.com/mcp/readonly",
      "tools": ["*"],
      "headers": {
        "Authorization": "Bearer ${GITHUB_TOKEN}",
        "X-MCP-Toolsets": "repos,issues,pull_requests"
      }
    }
  }
}

Type: `sse` (Server-Sent Events) — Deprecated

Deprecation notice: SSE transport is deprecated in the MCP specification. Use http (streamable HTTP) for new remote server connections. Existing sse configurations continue to work but should be migrated.

Connect to SSE-based MCP server:

{
  "mcpServers": {
    "cloudflare": {
      "type": "sse",
      "url": "https://docs.mcp.cloudflare.com/sse",
      "tools": ["*"]
    }
  }
}

Common Configuration Keys

Required for all types:

type: Server type ("local", "stdio", "http", "sse")
tools: Array of tool names or ["*"] for all tools

Local/stdio specific (required):

command: Executable command (e.g., "npx", "uvx", "docker")
args: Array of command arguments

HTTP/sse specific (required):

url: Server endpoint URL

Optional for all:

env: Environment variables object (local/stdio only)
headers: HTTP headers object (http/sse only)

Environment Variable Expansion

Use ${VAR_NAME} syntax for variable substitution:

{
  "mcpServers": {
    "sentry": {
      "type": "local",
      "command": "npx",
      "args": ["@sentry/mcp-server@latest", "--host=${SENTRY_HOST}"],
      "tools": ["*"],
      "env": {
        "SENTRY_HOST": "${COPILOT_MCP_SENTRY_HOST}",
        "SENTRY_TOKEN": "${COPILOT_MCP_SENTRY_TOKEN}"
      }
    }
  }
}

VS Code vs GitHub Copilot CLI Syntax Differences

Key differences between mcp.json (VS Code) and mcp-config.json (GitHub Copilot CLI):

| Feature | VS Code (mcp.json) | GitHub Copilot CLI (mcp-config.json) | | ------------------- | ------------------------------------- | --------------------------------------------------------------------------- | | Root key | "servers" | "mcpServers" | | Type values | "stdio", "http" | "local", "stdio", "http", "sse" | | Env vars | Supports inputs and envFile | Only env object with ${VAR} syntax | | Location | .vscode/mcp.json or global settings | ~/.copilot/mcp-config.json (or $COPILOT_HOME/mcp-config.json) | | Variable syntax | Can use inputs references | Must use ${VARIABLE} syntax |

VS Code example:

{
  "servers": {
    "memory": {
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-memory"],
      "env": {
        "MEMORY_FILE_PATH": "${workspaceFolder}/.github/memory.json"
      },
      "type": "stdio"
    }
  }
}

GitHub Copilot CLI equivalent:

{
  "mcpServers": {
    "memory": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-memory"],
      "tools": ["*"],
      "env": {
        "MEMORY_FILE_PATH": "${MEMORY_FILE_PATH}"
      }
    }
  }
}

Per-Agent MCP Servers

CLI agent files can declare remote HTTP MCP servers in mcp-servers frontmatter. This is the right surface when an MCP server is specific to one agent and uses the http transport:

mcp-servers:
  - type: http
    url: https://example.com/mcp
    name: example-server

Local stdio/local MCP servers cannot be declared per-agent — they must be configured globally in ~/.copilot/mcp-config.json.

Complete Configuration Examples

Multiple Servers

{
  "mcpServers": {
    "azure": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@azure/mcp@latest", "server", "start"],
      "tools": ["*"]
    },
    "github": {
      "type": "http",
      "url": "https://api.githubcopilot.com/mcp/readonly",
      "tools": ["get_issue", "list_repositories"],
      "headers": {
        "Authorization": "Bearer ${GITHUB_PAT}"
      }
    },
    "cloudflare": {
      "type": "sse",
      "url": "https://docs.mcp.cloudflare.com/sse",
      "tools": ["*"]
    }
  }
}

Docker-Based Server

{
  "mcpServers": {
    "notion": {
      "type": "local",
      "command": "docker",
      "args": [
        "run", "--rm", "-i",
        "-e", "OPENAPI_MCP_HEADERS={\"Authorization\": \"Bearer ${NOTION_API_KEY}\"}",
        "mcp/notion"
      ],
      "tools": ["*"],
      "env": {
        "NOTION_API_KEY": "${COPILOT_MCP_NOTION_API_KEY}"
      }
    }
  }
}

Setting Custom Config Location

| Method | Usage | |--------|-------| | COPILOT_HOME env var | export COPILOT_HOME=/path/to/dir — redirects entire config tree | | --config-dir flag | copilot --config-dir /path/to/dir — takes precedence over COPILOT_HOME |

Project-level MCP configs (shareable via source control): .mcp.json, .github/mcp.json, or .vscode/mcp.json — these take precedence over user-level definitions for conflicting server names.

Troubleshooting

Configuration not loading:

Confirm active config dir: run /session inside Copilot CLI to see the config path
Check mcp-config.json exists at that location
Restart Copilot CLI

MCP server not starting:

Verify command is available (e.g., which npx, which uvx)
Check logs in ~/.copilot/logs/ (or $COPILOT_HOME/logs/ if overridden)
Test command manually

Environment variables not expanding:

Ensure using ${VAR_NAME} syntax (not $VAR_NAME)
Verify environment variable is set: echo $VAR_NAME
Check variable is exported: export VAR_NAME="value"

Tools not appearing:

Verify "tools" field is present (required)
Use ["*"] to enable all tools
Check server initialization logs for errors

Converting VS Code to CLI Configuration

When migrating from VS Code mcp.json to CLI mcp-config.json:

Change root key: "servers" → "mcpServers"
Add "tools" field to each server (required)
Replace inputs with env and use ${VAR} syntax
Convert envFile to explicit env entries
Ensure type is valid for CLI: "local", "stdio", "http", or "sse"

Use Cases

Personal configuration: Default ~/.copilot/mcp-config.json

Session-specific servers: --additional-mcp-config flag (repeatable, JSON string or @file)

Project-level / team sharing: .mcp.json, .github/mcp.json, or .vscode/mcp.json — commit to source control

Agent-specific remote servers: Per-agent mcp-servers frontmatter (HTTP only)

Custom config location: COPILOT_HOME env var or --config-dir flag

Agent Skills: GitHub Copilot CLI MCP Configuration Management

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