I accidentally did ssh-add -d, trying to remove a certain key but it removed all of them from my ssh-agent. Do I need to re-add my key from authorized_keys or will it automatically happen next time I login with ssh -i me@wherever?
I'm afraid to logout and then be locked out of the system.
I tried typing ssh-add /home/me/.ssh/authorized_keys but then it asks for a passphrase and I don't know what passphrase it's talking about.
ssh-add is the client part of ssh-agent, it has nothing to do with granting access to hosts (which is done by adding the public key (.pub) to ~/.ssh/authorized_hosts on the server side). ssh-agent is a program which you use on the client side, the server side only needs sshd.
By invoking ssh-add -d, you have cleared a cached key from ssh-agent such that you have to re-enter your SSH keyfile passphrase next time you ssh to a system. You won't lock yourself out by clearing this cache. Simply run ssh-add (or ssh-add ~/.ssh/id_rsa for a specific keyfile) to remember the keyfile passphrase again for this session.
The -i option of ssh is only necessary if your private key is located on a non-standard location. ssh -i ~/.ssh/id_rsa user@host is nearly equivalent to ssh user@host since ~/.ssh/id_rsa is one of the standard places where SSH looks for a keyfile.
The reason why ssh-add ~/.ssh/authorized_keys prompts for a password is because it did not recognize an unprotected key, and thus assumed a password-protected key. In fact, the file has an invalid format so no password will work here.
See also the manual page ssh-add(1).
You can either copy the contents of .ssh/id_rsa.pub (which is your public key) and add it to the end of .ssh/authorized_keys or use ssh-copy-id localhost to let SSH do the copying.
Note that your key doesn't need to be in .ssh/authorized_keys unless you plan on SSH'ing into that computer using that key.
