Remove ROOT htmldoc macros, use Doxygen instead by `make doc`
Fixed unsigned int to int comparisons in TA2GoAT which appeared with verbose warning output
Added readout of central crystal and central Veto

Included in GoAT is the central crystal (for NaI or BaF2) and the central Veto (for PID or Veto). Changes to TA2CentralApparatus required as the particle class was being passed the hit index (0,1,2..) instead of the actual corresponding PID element (7,2,23...).
Removed Basel login from GoAT config
New default on MC files, 883 MeV Tagger file
Removed old class TA2Calibration

Old calibration class TA2Calibration is removed. This class is outdated
and replaced by a class TA2CaLib (already included).
TA2CaLib now using only standard analysis classes

TA2CaLib is now calling only standard classes (currently TA2Taps
and TA2CentralApparatus) instead of the My* classes which, in most
cases, were just bare-bones versions of old apparatus classes.
This change provides two benefits:
1. the same classes are now used for analysis AND calibration
2. these special case classes can be removed
Removing outdated My*** classes originally in place for CaLib

Still moving towards a concise Acqu set of analysis classes...
all classes designed only for running with CaLib have been
replaced by the standard classes. The old classes are now
un-used and therefore have been removed. Preliminary testing
shows no odd behaviour.
Updated data.2012.12 to include calibrations
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
Core: Added scripts for running on the farm
Fixed rootlogon to find libCalib.so in cmake version
Adding Calib databases, but commented out
Core: Add functionality to run single file from command line
FIX format string of printf() been misused as data string
User: Added EventID check to GoAT
Calib: Renaming config files
Calib: Getting rid of images directory in git