It's true that GitHub has a great API, but when you run your own server and have access to the running software and file system you get the best API for working

It's true that GitHub has a great API, but when you run your own server and have access to the running software and file system you get the best API for working on git repos there is: git. Or perhaps libgit2 and your favourite language's bindings. Subjectively, I haven't found GitHub's API to be great to work with, but this is because they use OAuth and OAuth is just needlessly complicated and inconvenient.