Herwig7_i: Fix the JO-Checker

In this MR we introduced a checker script that searches for command duplicates in the Herwig7 configuration files, this helps to validate changes and to make sure that no command is overwritten with a wrong value. The code contains a section to check whether there is more than one input file. This check seems to also find other file from Powheg with a very similar name. Since there should anyways never be more than one config file we want to remove this, because this currently breaks the ART tests as you can see here and here, marking this as urgent, since this could break the production when propagated into a release.