The idea was that for each diff box within the files, the atoms would have a backpointer to the current layer of diff_data (indicating the current section), but it is not actually needed to update the backpointer in each atom to the current diff_data. That is why the current code always points atom->d to the root diff_data for the entire file. Clarify by proper name. Constructs like atom->d->root->foo are redundant, just use atom->root->foo.