Package entrypoint allows inherited FastMCP transport and ignores CLI flags

[tony]

Problem

The package entrypoint calls server.run() without pinning the transport. FastMCP uses settings.transport when no transport is passed, so an inherited FASTMCP_TRANSPORT=http starts an HTTP server instead of stdio.

The entrypoint also ignores --help and --version; both start the MCP server.

Minimal local reproduction

$ FASTMCP_TRANSPORT=http timeout 3 uv run libtmux-mcp

Expected today: FastMCP starts an HTTP listener.

$ timeout 2 uv run libtmux-mcp --help

Expected today: starts the MCP server instead of printing help.

Upstream mechanism

• FastMCP uses settings.transport when transport is None: https://github.com/jlowin/fastmcp/blob/v3.4.2/fastmcp_slim/fastmcp/server/mixins/transport.py#L59-L60
• FastMCP then branches on the selected transport: https://github.com/jlowin/fastmcp/blob/v3.4.2/fastmcp_slim/fastmcp/server/mixins/transport.py#L64

Minimal fix

• Call server.run(transport="stdio") in the package entrypoint.
• Add a minimal argparse wrapper for --help and --version.

Acceptance criteria

• FASTMCP_TRANSPORT=http uv run libtmux-mcp still starts stdio, not HTTP.
• uv run libtmux-mcp --help prints usage and exits 0.
• uv run libtmux-mcp --version prints the package version and exits 0.
• Existing FastMCP manifest behavior remains unchanged.