I'd love to see the Flirc case have a IR window for GPIO setups, maybe you could even have a add-on similar to keymap-editor preform the same function as the windows program does for the USB Flirc. The other option would possibly involve an automated SSH that can place a config file of your remote into the proper directory. For now I have just drilled an opening into my case and plan on getting a piece of Ir acrylic to clean up the looks...