You can have team-based or private repos hosted by Keybase. Everything is encrypted and signed before it leaves your computer, and decrypted and verified when

You can have team-based or private repos hosted by Keybase. Everything is encrypted and signed before it leaves your computer, and decrypted and verified when your computer downloads it. But your local checkout of that git repo is unencrypted. It's just a normal repo. So Github Desktop has full access to it, like it does for all files in your local filesystem.