It seems to show this dialog two or three times. If I cancel it goes away and I'm still able to commit changes.
How do I prevent it from popping up each time and where do I find my passphrase if I have to reenter it and click "Remember to keychain" (which I've done before but will try again)?
Ricardo's solution is correct for macOS Sierra v. 10.12.2. I still needed to enter the passphrase the first time I ran the
ssh-agent
process, but not again after that. If you are doing this in a terminal instead of a GUI, be sure to either restart your session or reinitialize it with. ~/.ssh/config
In the latest version of macOS - 10.12.2/Sierra - this is an easy fix. Just edit your ~/.ssh/config and enable the UseKeychain option:
Save and solved.
If your ssh key has been protected with a passphrase, then you need to run an ssh-agent first, in order to avoid entering said passphrase for every connections.
See GitHub article "Working with SSH key passphrases".
If you don't have your passphrase anymore, it is better to re-create a new set of public/private ssh keys (protected, if you want, with a new passphrase), and publish that new public key on your GitHub account.