Small fixes and updates to FPGATrackSimHough output and flags

None of these changes should change the functionality/output of this part of the code. They are either clean-ups or additional flags/fixes.

Changelog:

• move output data writer to actual if clause in FPGATrackSimLogicalHitsProcessAlg.cxx
• fix typo in m_FPGASpacePointsKey handle key
• add flags and their handling for overlaying two input files (FPGATrackSimReadInput2Cfg and the flags wrapperFileName2 and secondInputToolN as well as the related tool)
• Remove leftover hard-coded value for DoHoughRootOutput flag
• Remove not yet functional secondStage config
• Add missing THistSvc for the HoughRootOutputTool
• Fix non-sensical value for bad member of FPGATrackSimMultiTruth class
• Fix non-sensical default value for m_barcode in FPGATrackSimTrack class

Tagging @brosser @imaznas @tbold @jahreda