It would be awesome to have some sort of tree view to this. I understand it is not easy to do with how this window was thought to work. So here is an idea: an optional sidebar to the existing differences view, which would show all the folders involved in the operation in a tree. On the right side, only the files in the selected folder would be shown. Clicking on the root of the tree would show all files (=what is shown now).
Besides better ordering, this would open up further possiblities, like one could even select/deselect a checkbox next to folders to skip all files in that folder.
