Parameters semantics are unclear

[PDoakORNL]

Parameters looks almost like an immutable native representation of the union of input parameters and defaults for unspecified parameters but violates this for:

1. Physics_Parameters::chemical_potential_
2. ...

We'd all benefit from parameters clearly containing the immutable run parameters such that it can be serialized to output hdf5 to unambiguous run parameters for reproducibility and reduce possibilities of difficult to find state related bugs.

Code that depends on this immutability:

1. Implemented disorder in the DCA Loop using the CT-AUX solver #365's approach to "quenched" disorder
2. ...

We need to gather information and ideally resolve this in the future.
I suggest a clear separation between immutable for run parameters and updating parameters of a run.
The DCALoopData seems like a likely place for the mutable parameters to be managed.