There are a few cases to consider. You have developed an internal combustion engine and a hoist that uses the engine to lift ships from the water. Either or both might or might not be patentable.
The hoist might be novel whether or not that particular engine is used in it. The engine might or might be obvious over previous internal combustion engines.
If the ...
Or, you could clarify in the patent you are only claiming the GitHub model and not the Git model, even though the Git model is explained.
You have to explain the basics for the derivative to be sufficiently discussed. Explicitly disclaiming them achieves your goal.
Git is distributed version control system software. It is not the first distributed version control system. Software is typically protected by copyright not patents. Git as an application is almost assuredly not patentable. It is possible that some specific elements within Git might have been patentable but they would need to meet all the requirements of ...