Running IDEA 11.0.2 on Windows 7, I have noticed that occasionally doing a CVS Update Directories command will re-create empty directories in my local modules. (These are directories left over from one of our many refactors.) They seem to appear/disappear almost at random when doing updates. I have verified that the "Prune Empty Directories" checkbox is checked, so I don't know what's going on.
Is anyone else experiencing this in Version 11? I found some old discussions in the forums but they were from years ago.