Example: Claude Code's .mcp.json

{
  "mcpServers": {
    "flyway": {
      "type": "stdio",
      "command": "<path to flyway>",
      "args": [
        "mcp",
        "-mcp.toolsets=develop_migrations",
        "-mcp.maxLogs=100"
      ]
    }
  }
}

See Configuration for what the command and args fields control, including the available toolsets.

If your AI tool supports it, you can instead point it at a config file's location with a flag, rather than needing to run it from the folder containing that file. For example, with Claude Code:

claude --mcp-config flyway-project/.mcp.json

Note: if you are using Flyway Desktop, check where it created your project's flyway.toml before starting your AI agent—it may be a subfolder of the folder you originally pointed Desktop at, not that parent folder itself. The MCP server doesn't need to be started from that folder, but the agent does need to know its path to load the project.

Other tools

VS Code (GitHub Copilot Chat) uses the same stdio server model, but its own file and shape: .vscode/mcp.json, with servers under a servers key instead of mcpServers:

{
  "servers": {
    "flyway": {
      "command": "<path to flyway>",
      "args": [
        "mcp",
        "-mcp.toolsets=develop_migrations",
        "-mcp.maxLogs=100"
      ]
    }
  }
}

The command and args values are the same regardless of which tool you're using—only the surrounding file format changes. Check your AI tool's own documentation for its exact config file location and format.

Checking this file into version control

Whether to check a config file like .mcp.json in, or keep it local (for example, via .gitignore), is up to you.

• If you check it in, avoid machine-specific local file paths in command. Use a bare flyway (relying on every contributor having it on their PATH) rather than something like C:\flyway-{version}\flyway.cmd, which won't exist on a teammate's machine.
• If you check it in, be aware that cloud-hosted agents supporting the same convention—not just AI tools running interactively on your own machine—may also pick it up and start the Flyway MCP server on your behalf. If that's not something you want, use your tool's own install instructions instead of a checked-in config file.