How does this work?
JK3 and JK2 both use the Ghoul2 (.glm) format for player models, but with different skeletons and bone indices. This tool remaps each surface's bone references from JK3 indices to their JK2 equivalents.
The vertex bone weights are stored as indices into the surface's own bone reference table — not the global skeleton — so they don't change.
Three JK3 bones have no JK2 equivalent: ltail and rtail (unused in player models) and lhang_tag_bone (mapped to lhand).