Since Xwin plays nicely with the system tray icon for exiting, is there any reason to listen for Ctrl-Alt-Backspace? I can think of two reasons -- compatibility with XFree86 convention across platforms, and preserving keyboard accessibility. I'm not sure that either one is very important here.
The least disruptive fix is probably to make Ctrl-Alt-Backspace invoke the same confirmation dialog that the system tray icon invokes.
Thanks, JT
