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by flamboyant_ride 1916 days ago
I use ssh key agent of keepassxc. This way only the public keys reside in the ~/.ssh and all the private keys can be made usable by unlocking my keepassxc db(and unusable on locking the same). Keepassxc stores the passphrases, additional notes if any for the keys.

With a properly configured gitconfig, .ssh/config I use different keys per domain(for different github accounts), different keys for different domains(ssh) and the like.