Merge pull request #1337 from RosettaCommons/aleaverfay/jd3_jobdist_jobqueen_interface
Fleshed out interface between JD3's JD and JQ when the JQ is interested in describing multiple-round protocols. The JQ describes the interdependencies between batches of jobs using a directed graph; each node represents a batch of jobs (all of which are independent of each other) and a directed edge from i to j implies that the jobs for node j will not be started until after the jobs from node i have completed.