Refactor for compound object manipulation

[dhblum]

This issue is to refactor methods of handling compound objects so that they do not get manipulated or reassigned unless explicitly specified. Such objects include exodata data dictionaries and the measurements dictionary. This is to prevent, for example, these objects from being assigned as a model attribute (e.g. parameter_data, weather_data, control_data, measurements, etc.) and further manipulated in a process not intended to affect it's use as the model attribute (e.g. for simulation or optimization using that model).

[dhblum]

This issue is related to #28.