We use Visual SourceSafe for our source control, and Ant for building. When we do a get-latest in Ant, we have it delete the local source tree and get the latest from VSS. IntelliJ handles this just fine; the files disappear and momentarily reappear, and IntelliJ will do some quick re-parsing and move on.
However, if we do a delete/get-latest on non-java files, IntelliJ will add them to the list of Changes and mark them with a dark yellow color -- I'm not sure if that's "ignored" or "hijacked". Suddenly having almost 400 files added to that list makes the Changes sub-window have zero utility for me. Is there a way to stop IntelliJ from doing that?