Add 2 new commands to run.py

[golnazads]

We need to have the following functionality:
python get_references -b <source_bibcode> (generates prioritized, merged list)
python get_references -b <source_bibcode> -a (returns all references with corresponding origin)

[ehenneken]

@golnazads I don't think we need this functionality in the pipeline, definitely not the first one. I have written a utility to do this type of extracting from the reference pipeline database, to support the integration into the Classic workflow. But in the (near?) future, all of this will go away when Honeycomb will take over all aggregating and merging of data.

[golnazads]

@edwin I have been working on this for a few days now and should have it done soon. I understand Honeycomb might eventually handle everything, but I do not think it can fully do what is needed here without the changes I am making to the database and pipeline. I am confident these updates will help bridge the gap until Honeycomb is fully in place.
@aaccomazzi