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LHCBGAUSS-874: Adds running over different EM physics lists and other small changes

Ryan Bernard Calladine requested to merge LHCBGAUSS-874.installandotherfixes into Sim09

Adds options to run over different EM physics lists, condenses rest of the options in to one file, rename some graphs for clarity, fixes bug causing the detailed monitor for MuonHitChecker to not be produced, adds lines to ensure scripts are installed and some general tidying up.

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