Privacy by necessity will use end-to-end encryption, as artifacts will end up being propagated on the network. This isn't however so easy for long-lived artifacts (eg. what happens if your key is compromised sometime in the future), and we will need things such as forward secrecy.

forgive the abbreviation, I was referring private repositories

It's not 1989 anymore, we have proper cryptosystems now. I don't have a worked example but elsewhere in the thread someone, it sounded like a dev, mentioned it's being worked on. You can encrypt for certain public keys and then only those people can decrypt the contents.