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When using ssh keys from gpg, there are no private key files on disk. The public keys are available from "ssh-add -L". Conveniently, users store the public keys in some ".pub" file under ~/.ssh (see e.g. https://serverfault.com/questions/906871/force-the-use-of-a-gpg-key-as-an-ssh-key-for-a-given-server; this is also necessary to use IdentityFile= in ssh itself). Thus public key files can't be ignored any more in list_ssh_dir_keys(). "ssh-keygen -Y sign" works nicely with a public key file if the agent has access to the private key.