First you need a good .gitignore file to make sure the correct files are in the repo and not any unnecessary files that have been produced by the Editor or compiling the project. A good example of that can be found on in the Mixed Reality Toolkit master files. You can download it here.
And on that topic, if you’re using Mixed Reality Toolkit in your project, have a look at my earlier post on including it as a submodule outside of your project. Keeps things clean, but also will slim down your repository while using the original version from the MRTK repo.