Le délire du jour avec gpg-agent et sa fonctionnalité agent SSH… ssh-add ~/.ssh/id_rsa -> Enter passphrase for -> Identity added -> The agent has no identities.

gpg-agent copies keys that you add with ssh-add to a special directory under ~/.gnupg (specifically ~/.gnupg/private-keys-v1.d with gpg2).

It seems, and I really think this should be reported as a bug, that if the key you're trying to add with ssh-add already exists in that directory it won't actually add the key to ~/.gnupg/sshcontrol which in turn means it won't be presented by gpg-agent. [...]

Once you remove the specific key and try adding again it should work. [...]