Little late to the party here but I am a heavy user of GitHub both personally and at work, and these recent changes have made it much less enjoyable, usable, and efficient.

I feel as though they were driven by some need to refresh the look of GitHub, but not by the need of the users. And this I think is the biggest mistake here.

If you have roughly 40,000,000 active monthly users — how many of those do these design changes serve? And how do they serve them?

That's what I'd be asking now if I was on your team.