@morgant I'm glad you like them and find those tools inspiring! I'd love to know what they inspired you into... (is it the MLVWM confirmation dialog?)
XFiles controlker script uses xmessage by default, but you can disable it.I personally do not like xmesage. I have tried to use a XTerm window before as a confirmation dialog, so the user can type Y/N and press Enter; but that's not mouse-friendly.
