Restructure `target.yml` schema to feature `primary` and `secondary` PDB structure keys

[dotsdl]

Instead of featuring top-level fields for pdb, iridium_classifier, iridium_score, dpi, and references.calculation, we would like these to be placed under a primary key, with alternate renamed to secondary.

This will make it clearer that references.calculation refers to the primary PDB structure, and not necessarily to the secondary PDB structure.

This is motivated given our swap of the primary PDB structure with its alternate for PDE2 in #52, in which the references.calculation list doesn't exactly apply to the new primary PDB structure.