Parameter handling using master phil

[nelse003]

Currently when parameters are needed in the current file, they are explicitly sources using:

process_refined_pdb_bound_ground_states(pdb, params=master_phil.extract())

Check whether there is a better way to do this?

[nelse003]

Look at:

restraints { output { include scope giant.jiffies.make_restraints.output_phil } include scope giant.jiffies.make_restraints.options_phil

in pandda.quick_refine

[nelse003]

Not explicitly sourced anymore