Refactor galaxy.workflow.run interface to use config object.
Number of ways to paramemterize workflow is a little bit sprawling already and it is about to get worse.
Refactor workflow API logic related to module population into run module.
Also moves runtime parameter override logic into that module as well. This is a good refactoring because it thins out a fat controllers (slightly) - but it is of particular interest because it makes it easier to recursively invoke potentially nested workflows from the workflow running module itself. It is still an open question whether that is desirable - see discussion on Pull Request #370 - but if it proves to be this can help enable it.