to account for changes to Cerenkov class

in THcDrifthChamberPlane::DefineVariable and output.def

  Default is to use new "invadc" parameters.  Use old style
  by setting Xtofusinginvadc=0

Lot's of changes to
 THcScintillator::ProcessHits
 THcHodoscope::EstimateFocalPlaneTimes
 THcHodoscope::FineProcess

  Rename ScalerLoc so it doesn't conflict with class of same name in podd
  Ignore .pcm files
  Makefile does version check for root 6
  Address warnings in hodtest.C

  Fix fptime formulae in output.def
  Remove unused parameter from THcHodoEff
  Remove undefined parameter from report.def

   H.hod.hgoodstarttime -> H.hod.goodstarttime

calorimeter.

negative side PMT signals from the HMS and SOS calorimeters.

    Changes in the Ycor method of the THcShower class, and in
    examples/PARAM/hcana.param input file.

Minimm value of normalized energy  fNormETot and minum value of number of
cherenkov photo electrons, fNCerNPE, is added to parameter files for the
calculation good scintillator event for tracking efficiency.
They are  optional parameters

fScinShould and fScinDid are set to 0 or 1
and only incrmented when Shower and Cerenkov detectors are setup.

If calorimeter and cherenkov is not added to SOS or HMS then it prints
a warning message and does not calcualte the efficiency for that
spectrometer.

Minimm value of normalized energy and minum value of number of
cherenkov photo electrons is added to parameter files for the
calculation of tracking efficiency.

  Variable found in a report template is first tested to see if it is a
  Hall C style parameter (in gHcParms).  If not, then tested to see if it
  is a global variable (in gHaVars).

  Clean up THcShower.h and THcShower.cxx.
  typedef vector<THcShowerHit*> THcShowerHitList by
  typedef set<THcShowerHit*> THcShowerHitList.
  Remove inheritance of class THcShowerCluster from THcShowerHitList.
  Define THcShowerCluster as THcShowerHitList, aka set<THcShowerHit*>.
  Remove inheritance of class THcShowerClusterList from
        THcShClusterList, a.k.a. vector<THcShowerCluster*> container.
  Define THcShowerClusterList as vector<THcShowerCluster*>.
  Rename THcShowerHitSet by THcShowerHitList.
  Rename HitList (related to the HMS calorimeter) to HitSet.
  Add operator< in THcShowerHit class, in order to have THcShowerHitSet
    objects to be properly sorted.

     Edit debug outputs in THcSHower and THcShowerPlane classes. Group
     outputs preferably by the end of methods, for smooth code
     flow. Structure tests of outputs for easy reading.

first track from the HMS shower counter code.

    Remove variables and code related to the maximum cluster of hits,
    and association of a cluster to the 1-st spectrometer track in
    THcShower.h and THcShower.cxx. Those were used for testing of the
    code, not needed any more.

track in Engine and the golden track in hcana.

      Add directory examples/gtrk_e holding the code.

Access the energy of the golden track from THaGoldenTrack.

    Include THaTrack.h in THaGoldenTrack.h.
    Add GetEnergy method in THaGoldenTrack.h.
    Define variable name "e" for the energy of golden track in THaGoldenTrack.C.

debug info should be suppressed in the main develop branch

shower counter's FineProcess.

       Remove THcHallCSpectrometer::TrackEnergies method.
       Add GetShEnergy call for each tack in THcShower::fineProcess.

In hcal_calib/hcal_replay_cuts.def:
   add one_clust condition;
   activate good_beta condition (defined for run 52949);
   define 2 versions of the Reconstruct_master cut, one for initial
   calibration and another for iterative calibration.

    Time difference variables now defined in output.def