MCP Tools Are Not Visible In The Agent

Symptom

Your agent host (Claude Code, Claude Desktop, Codex, or another MCP client) shows no autonomy / mcp__autonomy__* tools, or lists the autonomy server as disconnected.

Why

The Autonomy plugin doesn’t launch an agent — it registers an MCP server definition that the host connects to. That definition is a thin stdio proxy, not the runtime itself:


cat plugins/autonomy/.mcp.json


{
  "mcpServers": {
    "autonomy": {
      "command": "/Applications/autonomy (a7y).app/Contents/Resources/bin/a7y-cli",
      "args": ["daemon", "proxy"]
    }
  }
}

a7y-cli daemon proxy bridges MCP stdio to the already-running background daemon over its control socket. If the daemon isn’t running, the proxy has nothing to attach to, and the host sees either zero tools or a server that fails to connect. This is the most common cause of this symptom — not a broken plugin install.

If you registered the runtime directly instead of through the plugin (claude mcp add … autonomy-a7y mcp), there’s no daemon in the picture at all — that command line launches the MCP server binary directly over stdio. In that setup, a missing-tools symptom means the binary path in your config is wrong or unreachable, not that a daemon needs starting.

Fix

Confirm the command path

Check that the command in .mcp.json points at a real, executable path — the app bundle must actually be built and present at that location.

Check whether the daemon is running


a7y-cli daemon status

Start the daemon if it isn’t running


a7y-cli daemon start --dev

Doctor’s own remediation for a failed daemon attachment prints the exact start command for your state file, e.g. a7y-cli daemon start --state-file <path>, if you ran a7y-cli doctor first — see The daemon closes a request for what daemon-attachment failures look like in detail.

Reload the agent host’s MCP configuration

Restart the host, or use its built-in reload. For Claude Code:


claude mcp list

If Autonomy isn’t registered at all yet, add it directly:


claude mcp add --scope user autonomy -- "/Applications/autonomy (a7y).app/Contents/MacOS/autonomy-a7y" mcp

Verify


claude mcp list

Expect autonomy: … ✔ Connected. Then confirm the tool catalog is actually populated:


a7y-cli tools list

You should see 150+ tools, including accessibility_state, speak_text, screen_read_tree, and consent_request. If the host connects but the list is empty or stale, restart the host once more — some hosts cache the tool catalog per session.

See also Run the doctor before assuming the plugin itself is broken, and The daemon closes a request if tools appear but calls fail intermittently.