Remove Empty Folders enables or disables a task that runs in the background to delete any empty folders in your project.
This can be useful if you delete a folder outside of Unity but potentially have not deleted the folder 'inside' Unity. This is a common situation if you are using Perforce for example.
Simply select the menu option 'Assets -> Cleanup -> Remove Empty Folders' to enable this behaviour.
This will toggle the menu option from unchecked:
To checked:
Once enabled, this will monitor Asset Database changes and remove any Empty folders that it finds.
Note: this might cause frustration if enabled since it will delete any folders that is created manually as well (so you literally can't create folders if enabled).