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A while back I setup my git repo to connect using ssh and rsa keys using the instructions listed here: https://confluence.atlassian.com/bitbucket/set-up-ssh-for-git-728138079.html
After taking several months off from my project, I returned to find that I was now being prompted for my passphrase for the ssh key. I double checked the steps on that help page, and everything seemed in order, yet I was still prompted for my passphrase.
The issue was that the instructions said in Step 3, "If you are running OSX 10.6.8 or later you can skip this step." Since I was running 10.12.4, I skipped that step. However, it seems that my ssh-agent lost my private key, perhaps when I updated OSX to a newer version. Running "ssh-add ~/.ssh/id_rsa" fixed the issue.
These instructions are great, but might be made slightly clearer by telling all users to execute step 3, just in case.