Stdio MCP servers discovered by the plugin loader now have their tools
automatically registered as CLI subcommands. The runner dispatches
stdio:// virtual endpoints to the local StdioClient subprocess instead
of the HTTP transport, enabling plugin tools to be invoked directly
from the command line (e.g. `dws hello greet --name Peter`).
Also fixes a bug where plugin endpoints registered via AppendDynamicServer
were overwritten by the subsequent SetDynamicServers call in
loadDynamicCommands, and a context lifecycle bug where stdio subprocesses
were killed immediately after startup due to a short-lived timeout context.
