If you got a message that you aren't allowed to delete something in the repo, then you were deleting something that you shouldn't have, so that's already worrisome that you thought you should delete those things. There is no need to delete anything. You've got 2 to 3 years of dev work, focus on that first. You can use whatever folder structures you'd like, except where otherwise noted, like with the dynamic2 folder for characters, and the folder for terrain textures and dynamic details to show up by default.