I suspect that the (rather complicated) branching information was lost, though for my purposes that's fine. I just want to be able to apply, test, and remove patches from the mozilla head. (Mmm my own custom firefox and thunderbird).
If I cared more, my interpretation of the git docs suggest that it supports multiple branches within a single repository. Most of the other distributed version control systems view each repository as a single branch.
Now I just need to get ccache working with the mozilla build system so it doesn't take 3 hours to build.