When doing a recursive diff between two folders, Diffzilla seems to be scanning the files in a directory listed in the "Exclude filespecs" list. Specifically, I see this with .git/. There are loads of files there, none of which are relevant, but the display shows them during the scan. The files don't seem to be compared, but the list building step takes longer than necessary, especially if the filesystem is remote (e.g. mounted with sshfs). It should be possible to skip everything under the matching directory name.