The biggest problem I have with the Github auth flow is around organizations. An organization can prevent my apps from accessing its repos, but I can't deny an app permission to access organizations that I don't want it to. As a freelancer, when some client uses a Github app to do something, I have to give that Github app access to all of my other client's organizations, because Github won't let me disable them.
I would say make per-client Github accounts, but that's stupidly painful to manage too. It would be nice if they could do what Google does with multiple accounts being logged in being supported (though, that implementation has warts, too).
Yes, as a contributor or member of a few different technical groups with GitHub organizations, I feel the same way. Those groups don’t want me using app X on their repos, and neither do I!
