But we don't change things just to change them. We still use the nif file format, because it worked fine for what we're doing and our modders know it well. We still use some middleware that we like, such as Havok. We're not just using their physics this time, but their animation system, Havok Behavior. It makes a dramatic difference in how the game looks and plays.
So, they are using Havok for the animations, but use the NIF file format for the resources. That would make sense. Their content management system, tools, and animation library are most likely based on NIF and thus switching to Havok's format is counterproductive. As an added benefit modders can still use the tools they are used to. It also explains why some Gamebryo references can be found in the executable: A part of Gamebryo's engine was required for converting the resources from the NIF format to something Havok can use.