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ISF_Validation: Fix for test_RUN3_AF3InputParamFiles.sh (ATLASSIM-6904)

John Chapman requested to merge jchapman/athena:FixATLASSIM-6904_main into main

Configuration was being applied to a public instance of LArPileUpTool rather than the private instance owned by PileUpToolsAlg.

Also added the workaround for running RAWtoESD using legacy config.

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