Working as a developer, too often I have had to refrain myself from updating a plugin or theme, because I don't know if the previous developer modified it to fit the clients need (or even if I did it my self, many months ago). Thus I ask: is there a way to mark modified plugins and themes as modified, so that I know when to update or not?
One way to do it would be to keep two copies of each plugin and theme, one in an "originals" folder, and one in a "modified" folder. Thus by comparing the modified and original versions, WordPress could tell if the plugin or theme was modified or not.
This approach would also open up the possibility, with some extra hard work, to show which lines were modified in a plugin or theme! That would be SO useful! Too many hours are wasted diving into the code of a plugin or theme, looking for that tiny fuckhack that screws everything up. Besides, knowing which lines were modified would make it so much easier to update modified plugins or themes, because one could simply copy and paste the modified code, make a few mental notes, then update the plugin or theme, and manually restore the modifications.
I realize this features would imply quite a lot of work, but hey, I think it would be damn worth it.