In Eclipse when you press Command-Shift-R (Open Resource), you end up seeing the same resource a few times -- when it e.g. gets copied into a location in the workspace by your build tool (e.g. maven, ant).
I was looking for a solution for some time now and way playing with working sets for this purpose.
Rob Mayhew obviously has one:
Now the "only" thing left to do is to mark those target directories as derived -- after each clean up of those folders.
Someone on the net even wrote the right script