Simulation: Remove more legacy configuration modules
This merge request removes a number of legacy configuration modules:
- DigitizationFlagsHelpers
- JetRec_FastCaloSim
- OverlayHelpersLegacy
- FatrasTrackingGeometrySvc
- HitsFilePeeker
and cleans up references to SimFlags and DetFlags in commented out code (this commented out code should remain in place for now).