extracting functions to allow the ews job dir and the config dict to be created without needing to run the pipeline - allows epi fitting to retrieve these values if the peipeline has already run

making the running of epi plotting dependant on whether config had been provided. Modifying tests to stop using epi outputs which are no longer included

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