Yes, BP cleans the remote working directory after successful updates or deployments. However, an unsuccessful operation could leave files there. In all cases, BP always leaves a couple/few log files in the folder, and I would recommend that you do not remove these since they contain the history of update operations. If you do decide to remove these, it won’t break anything but you’ll lose some of that history information. If you want to delete the entire directory you may use ‘Tools > Delete remote working directory.’ If you want to delete only certain files/folders in it, then you would have to use a custom command.
-Doug