Recently, I took the plunge and upgraded from El Capitan to Sierra and
kept getting prompts like the following every time I tried to do a
Enter passphrase for key '/Users/my.user/.ssh/id_rsa':
I tried the standard method of adding the key to the ssh-agent with:
ssh-add -K ~/.ssh/id_rsa
However, every time I would open a new shell, I would get the same prompt for my passphrase again. Luckily, I was able to find the answer in a comment on StackOverflow:
Host github.com ... UseKeychain yes
This seems to have fixed the issue and I no longer have to deal with the incessant prompts for my passphrase.