An upstream change in pam_ssh-2.1 requires you to add a new subdirectory: ~/.ssh/login_keys.d/ and in that directory you must create a symlink to ~/.ssh/id_rsa in order to be able to ssh in by using your ssh passphrase instead of your password.
When you login (or ssh in) you will now see a prompt for "SSH passphrase:" instead of the old "Password:" prompt. This could be confusing if you don't use an ssh passphrase, but your password will still be accepted as usual. I'm wondering what problem this change is solving for us. I already know at least one problem it created ;)