git-annex has local encryption for specific remotes (i.e. you can add a remote and say ‘encrypt data before putting it there’, and then add another remote, such

git-annex has local encryption for specific remotes (i.e. you can add a remote and say ‘encrypt data before putting it there’, and then add another remote, such as a USB key, and don’t encrypt data on it). I haven’t used it in a while, but it is becoming more and more mature, methinks.