My solution is to create another folder like “~/Documents/Projects” (because I have no free-standing documents really) and use it as “my” dir. All other paths are known to apps and will be abused.
I do the same thing (on win, mac, and linux). Except I call it "proj" because I'm lazy. In fact, I split it between github and proj because the former is already backed up, but the latter is not.