Clean up submodule GIT_DIR workaround

In https://github.com/dotnet/source-build-externals/pull/27 and https://github.com/dotnet/source-build/pull/2906 I introduced a workaround to prevent git from erroring out while applying patches in source-build-externals by forcing it to treat the repo as a non-git directory. This isn't an ideal workaround and in the unified build VMR we should be able to implement something better (probably by not removing the `objects` directory and treating the submodule as a real submodule).