When you delete the last file in a directory from Git in the command line (git rm dir/file.txt
), Git itself automatically deletes the whole directory.
In other words: IDE behaves the same as Git does.
Can I prevent this?
Nope. At least not at the moment.
http://youtrack.jetbrains.com/issue/IDEA-75590 -- watch this ticket (star/vote/comment) to get notified for any progress.