While git internally uses a pretty loose system for connecting different model concepts that has always seemed more like a concession to the storage medium than a desired step. If git existed on an already ACID compliant system instead of trying to build one out of the filesystem itself I don't see a reason to keep all the references as loose as they are. If you can cascade changes with confidence you can likely just switch to using standard surrogate keys for linkages and allow the data to normalize more fully.

The core model objects in git are all pretty straightforward and their interactions well defined.

Fossil really has it all.