Core: Fixed Ladder reconstruction of MC events
Added the ability to replace an input prefix instead of just append to it, as well as setting the default output directory to be that read from the top-level acqu setup file with the Directory line
Creation of a new macro, FinishBatch, that works a little better for batch/farm running. Also edited the MC config files to use this new macro, and to run in batch mode
Added new set of config files for most recent data, with new TAPS numbering