Refactor name of from/to_pb_message and from/to_pb_value to be descriptive one is used in the workflow definitions and the other in params_dict

`{from,to}_pb_message` are used for workflow definitions while `{from,to}_pb_value` are used to pack a params_dict value into protobuf Struct to accompany a JobSubmission. These names are not descriptive at all and should be altered to showcase their intended goal.