git-annex mostly does not use encryption. Anyone with access to a git repository can see all the filenames in it, its history, and can access any annexed file contents.

Encryption is needed when using special remotes like Amazon S3, where file content is sent to an untrusted party who does not have access to the git repository.

Such an encrypted remote uses strong GPG encryption on the contents of files, as well as HMAC hashing of the filenames. The size of the encrypted files, and access patterns of the data, should be the only clues to what is stored in such a remote.

You should decide whether to use encryption with a special remote before any data is stored in it. So, git annex initremote requires you to specify "encryption=none" when first setting up a remote in order to disable encryption.

If you want to use encryption, run git annex initremote with "encryption=USERID". The value will be passed to gpg to find encryption keys. Typically, you will say "encryption=2512E3C7" to use a specific gpg key. Or, you might say "encryption=joey@kitenet.net" to search for matching keys.

The encryption design allows additional encryption keys to be added on to a special remote later. Once a key is added, it is able to access content that has already been stored in the special remote. To add a new key, just run git annex initremote again, specifying the new encryption key:

git annex initremote myremote encryption=788A3F4C

Note that once a key has been given access to a remote, it's not possible to revoke that access, short of deleting the remote. See encryption design for other security risks associated with encryption.