Add a --silent command line option. This would function just like the --auto option except if the files can't be auto merged KDiff3 will exit with a non 0 exit code instead of displaying the GUI. 

This would make KDiff3 more useful for scripting. A user can already have a script continue if KDiff3 is able to auto merge a file, but if the file can't be auto merged a script will just hang while KDiff3 waits for a user to resolve the issue. This option would return control to the calling script and let the user decide what action is appropriate.