I just wanted to let everyone know that after some testing I can confirm that whatever is not in your cooked mod’s folder is deleted from your mod’s Steam Workshop. This should allow you to cleanup any assets that you uploaded to your mod before and are no longer using. To do this all you need to do is go to C:\Program Files (x86)\Steam\steamapps\common\ARKDevKit\ModTools\Output and delete any folders you wish to clean up. Then cook and upload your mod again. Steam will not delete any files already in a subscriber’s mod folder, but if they delete the files or are an entirely new user, steam will only give them the files you last uploaded.
The outcome we really want is for unused files/folders to be deleted from subscriber (client or dedi servers) installations… so I guess we are half-way there (i.e. at least the Unreal → Steam file management is fixed)?
Gets to be dangerous when deleting files off of a user’s computer just because it exists in a folder, but yes its a step in the right direction. If for whatever reason as a modder you know it is causing problems in your mod, notify your subscribers they need to delete the folder out of their client.