adding ability to set additional values to the run config from the command line args (if not already present in the config json)
modifying the epi processor to look for CalculationSpanDays in both the config json and the command line args, as preparation for use with the Epi fitting, which will pass calcspan as an arg

making processor components pass their shortname in - rather than relying on the short_name map to know about all components

adding a check for loading resource files before all partial integration tests begin. Allows the user to spot if they have not set their working dir correctly