FFS is indeed an excellent tool - I'm using it as a replacement for the old Fileware "FileSync" app, which was also excellent but has not been updated for many years now and creaks a lot with Win7 and the huge files of today.
I have noticed one quirk, though, which could cause you to delete files unwittingly. Lets say you wanted to use FFS to isolate the unique (or unequal) files within two similar folder branches. You would probably use the buttons at the bottom of the list to display just the EQUAL files and then go ahead and delete them, leaving only the unique ones, right?
When you highlight all the equal things and hit delete, FFS pops up the "are you sure" dialog, showing a list of all the things it is going to delete - all the equal files and folders. However, watch out! If that list contains a FOLDER, FFS will delete the ENTIRE FOLDER, not just the files within it that are equal. So you could be deleting unique files and FFS doesn't warn you.
I think maybe an option is needed to exclude folders from the display, so it only leaves the files showing?
Another great option would be one to remove empty folders from either/both sides.
Possibility of deleting files you didn't expect to
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