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I guess it's a private repo...

For many dotfile configs such as text editors, aliases or else not involving security, I personally don't care if it's public. Take this example https://github.com/AzogMugen/shortcuts-config/tree/master/ho...

Where does their comment indicate they commit secrets?

Perhaps SSH/GPG private keys are .gitignored?

I protect my ssh keys with passphrases, and then load the keys using ssh-add.