GMOnline would read a text file every second to check for commands and data. You could write QUIT to cause GMOnline to quit.
However, a much more clever way (possible with SC games) to have an external plugin communicate with your game is to use a socket. Open a socket and have it listen on a unique port such as 56237 (don't use that one, make up your own 5 digit port for the plugin). Then you LAUNCH the plugin, which will attempt to connect to localhost (127.0.0.1) on the same port.
When you want to quit the plugin then you can just send a quit command somehow (you could implement EZProtocol into the plugin if you wanted to, so it would be as easy as sending commands with an easy socket).
