Ulrik Sverdrup has written https://github.com/blake2-ppc/git-remote-gcrypt, which allows using gpg encrypted ssh remotes with git. The same idea could be expanded to other types of remotes, like S3. I’m excited about adding encrypted git remote support to the assistant! (source)

This is very exciting. I am tired of using s3ql for this purpose rather than just having all my metadata and data stored in an encrypted git remote on the same machine where, at present, only my encrypted data is stored.