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These days I'm mainly doing development inside VM's. Previously I was embedding Github key to each VM, but since I setup Secure Enclave (with Secretive), I'm only forwarding it's agent to VM and each git action on origin now requires approval using fingerprint reader. I think this a good way to prevent malware from gaining access to github
Why not use PAT?

I’ve grown to appreciate ssh should only be used with git for signing commits and as a deploy key (eg in a CI system).

I always use https for day to day git operations. My keys reside in gopass and are extracted by gopass-git-credential when needed by git.

I use that within devcontainers

https://github.com/gopasspw/git-credential-gopass

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