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GitHub always freaks out at me when I include text that even looks like a PEM cert. Too bad they can't scan for AWS key / secret variables too.

They do, this was likely in a private repo which isn’t scanned.

I pretty sure had a PEM cert in a private repo and was alerted. Is this in their TOS somewhere?

You can opt into secret scanning on private repos, but it isn’t default when I last used it.