Merge pull request #1678 from RosettaCommons/aleaverfay/sfxn_from_option_collection
Initialize ScoreFunction and its derivatives from a local OptionCollection
In particular, the EnergyMethodOptions class previously read from the global option system in its constructor. Now, when you call get_score_function with a local OptionCollection object (as people will do in JD3), the OptionCollection is passed along through the ScoreFunction to the EnergyMethodOptions object, and the EnergyMethodOptions object reads from this OptionCollection.
This PR brings in two unit tests that ensure that no options read during ScoreFunction initialization from the local option collection are undocumented. The main documentation function is the static method EnergyMethodOptions::list_read_options.