git-annex can communicate over the Tor network. This allows direct communication between git-annex repositories, no matter where they are located.

A git remote using tor has an url that looks like tor-annex::2lssjzicvsxkdc2v.onion:19984

To set this up, use ?git-annex-enabletor and git-annex-p2p, and run git-annex-remotedaemon to serve the Tor hidden service. It's explained in detail in peer to peer network with tor.