Modifies prepare_scenario and prepare_run function in cli to only use the upper level Store class and not the lower file store YamlConfigStore class.
Modifies prepare_scenario and prepare_run function in cli to only use the
upper level Store class and not the lower file store YamlConfigStore class.

nismod/smif,tomalrussell/smif,nismod/smif,tomalrussell/smif,nismod/smif,tomalrussell/smif,nismod/smif,tomalrussell/smif