The easiest way to work with it is to fork Core on GitHub, then then commit, push to my-fork and Pull Request. Then you're all done 
(You do need to update the submodule manually for everybody else - just pull from origin, then go to the root directory for MCServer and commit it as if it was a file. You don't need to worry about this as people can do it later, just for timing.)
Code:
git remote add my-fork (your URL here)(You do need to update the submodule manually for everybody else - just pull from origin, then go to the root directory for MCServer and commit it as if it was a file. You don't need to worry about this as people can do it later, just for timing.)