managing-mcp-servers

Managing MCP servers in ThinkRail

ThinkRail uses pi's built-in MCP support but has no pi executable. Never run pi mcp add, pi mcp login or other pi commands; edit the configuration files and point the user at Settings › MCP servers for everything that needs them.

Where servers are configured

• User level — pi's agent directory, usually ~/.pi/agent/mcp.json: available in every project.
• This repository — .pi/mcp.json in the worktree, tracked in git. A server defined here does not run until the user approves it in Settings, and any later change to its entry needs approval again. It only loads when the user trusts the project.

Both files use pi's format:

{
  "mcpServers": {
    "docs": { "url": "https://example.com/mcp" },
    "browser": { "command": "npx", "args": ["-y", "@playwright/mcp@0.0.83"] }
  }
}

• Pin package versions in args; never @latest.
• Never write a secret into either file. Reference it as ${ENV_VAR} (from the host's environment) or !command (the command's output, for example !gh auth token), or let the user sign in.
• exposure: deferred (the default here — load the server's tools with tool_search first), direct (a few always-useful tools), or hidden. codemode is treated as deferred.
• Prefer the user-level file for personal servers; only put a server in .pi/mcp.json when the user wants it shared with the repository.

GitHub

GitHub is a recipe, not a preset: its hosted server, authenticated with the user's GitHub CLI sign-in. Add it to the user-level file (Settings › MCP servers offers the same entry under Paste JSON):

{
  "mcpServers": {
    "github": {
      "url": "https://api.githubcopilot.com/mcp/readonly",
      "headers": { "Authorization": "!t=$(gh auth token) && echo \"Bearer $t\"" }
    }
  }
}

• /readonly is GitHub's documented read-only mode (same as an X-MCP-Readonly: true header). Use https://api.githubcopilot.com/mcp/ only when the user asks for tools that change data.
• The header command runs each time a chat connects. While gh is logged out it fails instead of sending an empty token; the user runs gh auth login in a terminal.
• Unverified: whether GitHub accepts the GitHub CLI token's scopes for every toolset. If the server rejects it, ask the user for a token in an environment variable: "Authorization": "Bearer ${GITHUB_TOKEN}".

After editing

The host reloads idle chats on its own and a busy chat picks the change up when it is idle. Tell the user when a step is theirs: approving a repository server, or Sign in for a server that uses OAuth (both in Settings › MCP servers). Do not ask them to restart ThinkRail.

Using MCP tools

• Tools are named mcp__<server>__<tool>. For a deferred server, call tool_search to load them.
• Subagents cannot call MCP tools: call them yourself and put what the subagent needs in its task.
• ThinkRail asks the user before a call that may change data. A denied or cancelled call is final for that call; do not retry it without asking the user first.