Hi!
At the moment, if you add folder A and folder B to the folder list for comparison, the comparison occurs between ALL files in both folders, A and B (including files in A between other files in A, and the same thing for folder B), but sometimes (many times, actually), it would be extremely useful to be able to choose to ONLY compare all files in A with all files in B, as opposed to also comparing files within the same folder. This will dramatically shorten the scan time in this type of situation.
I hope I managed to express things clearly.
Last but not least, thank you ever so much for making this wonderful piece of software and giving it away freely. You are a great man.