Make libgit2 an actual submodule - #1017

This PR should hopefully help us track how libgit2 changes from version to version by making it an actual submodule of the library.

I added scripts to automate updating any submodules of the repo so hopefully if we add more submodules (which I think I will) they should just be dropped in and work (famous last words).

Currently we do the following for updating submodules during a lifecycleScripts/install:

• If you have a submodule that is not initialized we will initialize it recursively for you.
• If you have a submodule that is initialized we don't do anything to it.
• If you have a submodule that is on a different commit we warn you about it in the console and don't modify the submodule.
• If you have uncommited changes to a submodule we stop building/compilation and notifiy the user that they need to resolve this before we continue.

During a generate we just check to see if the submodules are all good (i.e. all initialized, on the correct commis and no work dir changes) and if any aren't we'll put up a warning in the console.