Back when drupal was in CVS I had my sites in a git repository and then pulled in core and contrib via CVS. The two systems happily co-existed and I could track changes to everything and make patches to contrib modules. Now with git I am unsure whether to just download contrib and core and check it into my site's git repository, or maybe use submodules?
I am wondering if there are any best practices on this yet? I am particularly puzzled about how to have core as a submodule if my repo uses drupals root directory as its own root?