Occasionally I run into an issue where if I do a refactoring on my git project in eclipse that requires renaming a folder those folders will still show up on the github website (completely empty) even though they are not in the local workspace.

It appears that happens only when I commit the changes through eclipse via EGit via JGit. It appears to be https://bugs.eclipse.org/bugs/show_bug.cgi?id=314105

Anyway the easiest way to fix this is to do a commit outside of eclipse via the command line git. Once pushed to the remote the empty folders disappear.