vertex groups and matrices

I've spent countless hours trying to create these from vertices and bone indices. Anyone have any clue on how to create these from scratch? (Milkshape3d doesn't use these, CharacterFX doesn't use these)

I know that there is a vertex group for each vertex which points to a matrix. The matrix points to a bone reference (multiple referencing is....pretty hard to figure out), but Blizzard doesn't have a matrix for every bone.