Well, while I've already implemented your request (no nightly build yet), I still wonder about other messageboxes which can appear during a rebuild.
I've added a batch option to avoid messageboxes during a batch run and currently "dead end" boxes where you can only tick "OK" or "OK/CANCEL" are not shown (e.g. disk full or your "destination is a subfolder of the source -> skip" message).
Now there are some YES/NO messages where I still have to decide which answer would be the best to use when no prompt is shown:
I'd use "yes" for the following:
Error while rebuilding: file x to archive y Do you want to stop?
Error while adding: file x to archive y Do you want to stop the rebuilding process?
Destination: x doesn't exist! Should it be created?
I'd use "no" for the following:
Scanner and Rebuilder mergemodes differ! Do you want to continue?
Scanner and Rebuilder use different methods to store bios roms Do you want to continue?
SysDefPaths mismatch between Rebuilder and Scanner. One of them uses SysDefPaths while the other doesn't. Do you want to continue?
At least one add-path points to a ROM-path. Additionally you got (adv) remove options enabled. Are you really sure you want to continue?
Your rebuilder source points to a ROM-path. Additionally you got (adv) remove options enabled. Are you really sure you want to continue?
No real idea about the following though....it's for the special option "remove only"...
No files will be rebuilt but matching sourcefiles will be removed. Be warned: No backup of these sourcefiles will be done, they'll be gone! Are you sure to do a remove-only run?