Fix a bunch of shit.  Clean up the mess I made by removing the
unintuitive constructors on subclasses of AbstractProtocol.
Add sequence_number back to job.  Fix a bunch more fallout.

Merge branch 'attributed-protocols' of
https://hellblazer@github.com/ChiralBehaviors/Ultrastructure.git into
attributed-protocols

Conflicts:
	animations/src/test/java/com/chiralbehaviors/CoRE/meta/models/JobModelTest.java