I'm about to sound crazy.

Github's problem is that it isn't a SPA. It is a massive Ruby on rails project that is all server-rendered. Everything you do needs to be synchronous and almost everything requires a reload. A react or angular app with great restraint would be dramatically faster at all of this as viewing a file is just an API call - not a page reload. They are stuck with their hands tied as loading large data would cause the whole page load to be delayed - thus silly limits.

Many things should not be webapps... but an app on the web like this...probably should.