Step one: removed the tallest tent pole by fixing the ValidationTarget cache. Not everything was being cached. In fact, little to none of it was. Implementing this sped up the final step that counts on this by 10x. The 11000 strong bundle went from 73 seconds to 7.3 seconds. The overall time remains fixed at 1500 seconds. Not sure if the 73 seconds were simply redistributed or if that is just normal variation of an uncertain process (depends on network download times).

TargetExaminer does not need to read the same file over and over. Do it once, collecting the information needed and then store for later. Yes, another cache.

The look in referential integrity was overly complicated. Reduced it to a HashSet.contains() which really speeds things up.