I am currently using rsync.net to keep my notes in sync, both git repo and the content (gpg encrypted) is stored there. Instead of creating two other repos on a server that I have which has git-annex installed where I can actually use remote daemon. Is it possible to create a repo containing both the git repo and the content encrypted from the command line?
Why not go all the way and encrypt the git repository stored on the remote server too? gcrypt
When you have git-annex-shell installed on the remote server, the remote daemon should work for gcrypt repositories as well as normal non-encrypted git repositories.