Modified so that the fGoodPosAdcPulseTime, fGoodNegAdcPulseTime
  or fGoodAdcPulseTime is set to kBig

Modified THcShowerRawHit::SetReference to takeADC signals

Modified THcTrigRawHit::SetReference to take ADC signals

Modified THcShowerArray::ProcessHits so that fAdcTdcOffset add to frAdcPulseTime

Modified THcShowerArray::ReadDatabase so that defaults for fAdcThreshold etc
  are before gHcParms->LoadParmValues

Include methods for FADC conversions and apply to non-raw data objects in THcRawAdcHit

Add raw pulse time data object to Cherenkov detector classes

Add raw pulse time data object to shower detector classes

Add raw pulse time data object to hodoscope detector class

  Cache the Cherenkov detector and parent pointers in Init

  For both the layers and the array part
  Correct calculation of coordinates of the Array modules in the
    calorimeter effciency calculations.

   Gets rid of vars.push_back(RVarDef ... stuff

Also do some whitespace cleanup

  Add "Good" variables to calorimeter class
     occupancies and multiplicities
     required to pass time and threshold cut
  Change some variables from arrays to vectors
  Modify how thresholds are calculated
  Remove obsolete variables: posadchits, negadchits
  Add flash adc debug flag
  Correctly delete pointers in destructor

  Add "Good" variables to calorimeter class
     occupancies and multiplicities
     required to pass time and threshold cut
  Change some variables from arrays to vectors
  Modify how thresholds are calculated
  Remove obsolete variables: posadchits, negadchits
  Add flash adc debug flag
  Correctly delete pointers in destructor

THcShowerArray
1) in ProcessHits methodfFixed mistake in index of fThresh
   was using padnum instead of padnum-1
2) add parameter pcal_arr_AdcThreshold so that threshold
   can be set by a parameter. Default is zero which gives
   the best resolution.

THcShowerPlane
1) Added the parameter cal_AdcNegThreshold and cal_AdcPosThreshold
   so that the threshold can be set through a parameter
   Previously it was hardcoded.

Main purposes:
1) Add the possibility of multiple ADC hits per channel and
   select best ADC by a time window.
2) Change ProcessHits method in ShowerPlane and ShowerArray to only
    fill "raw" TClonesArrays.
3) Add CoarseProcessHits method to ShowerPlane and ShowerArray
    to fill the "good" data arrays from call in THcShower:CoarseProcess
4) Moved code to fill Track object with energy from FineProcess
   to CoarseProcess so that the Track->Get(Energy) can be used by other
    detectors in their FineProcess.
5) FineProcess loops over Track object add gets Track energy
6) Add AdcErrorFlag TClonesArray to be filled to check for
   problems with FADC




THcShower.h
1) Add methods GetADCMode(),GetAdcTimeWindowMin(),GetAdcTimeWindowMax()
    so that the ShowerPlane can access these parameters
2) Add parameters ADCMode,fAdcTimeWindowMin,fAdcTimeWindowMax
3) Add variables
   fNclustTrack : NUmber of cluster that matches best track
   fXclustTrack : X pos of cluster that matches best track
   fXTrack      : X pos of best track that matches cluster
   fEtrack  : Cluster energy associated with best track
   fEtrackNorm  : Cluster energy/Track momentum associated with best track
THcShower.cxx
1) Add calls to THcShowerPlane and THcShowerArray CoarseProcessHits
    in CoarseProcess
2) Moved filling of Energy in Track object to CoarseProcess
3) In FineProcess get the "best" Track object and match
   Track energy and trajectory to cluster.

THcShowerArray.h and cxx
1)add parameters fADCMode, fAdcTimeWindowMin and fAdcTimeWindowMax
2) Add method CoarseProcessHits
3) In ProcessHits fill fPosThresh and fNegThresh with a fix
    value of 250 integrated channels above pedestal.
     Need to make this a parameter.

THcShowerPlane.h and cxx
1)Gets fADCMode, fAdcTimeWindowMin and fAdcTimeWindowMax from THcShower
2) Add method CoarseProcessHits
3) In ProcessHits fill fPosThresh and fNegThresh with a fix
    value of 250 integrated channels above pedestal.
     Need to make this a parameter.

 - Added new leafs to the hodoscope tree.
 - Added new leafs to the aerogel tree.
 - Added new leafs to cerenkov tree.
 - Added new leafs to the shower tree.

Left all the old leafs in there. Will need a careful cleanup...

The new class THcRawAdcHit is meant to represent the raw ADC hits. The
logic with dealing with ADCs has become quite complex now and it would
have to be multiplicated across all detectors that have ADC
channels. While this by itself is not such a big problem, fixing
possible bugs in multiple places is.

I also redesigned the THcRawShowerHit class to use the new
THcRawAdcHit. The redesign was due anyway, so I took the opportunity.

I also had to modify THcShowerArray and THcShowerPlane. They still
need some work to use the the new flash 250 data, but changes were
necessary anyway.

Minor fix 01.

  A shower counter hit can now be multiple samples, with a different
  number of samples allowed for positive and negative tubes.
  GetData(signal) now returns the sum of all the samples.  This should
  still be compatible with fastbus ADCs as they are a single sample
  (which is already the integral.)

  Modify THcFormula and THcParmList to match changes to THaFormula
     (needed for reports)
  Small changes in THcInterface and detector classes for compatibility
     with new OO decoder and podd 1.6

     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.

    Add fdbg_raw_cal flag in THcShower.h.
    Initiate fdbg_raw_cal with engine's hdbg_raw_cal in THcShower::ReadDataBase.
    Supply calorimeter debug flags to otherwise free print-outs in the
    THcShower and THcShowerPlane methods.

Re-arrange, modify and make more detailed comments in the Shower*.h header
files. Add more comments in the Shower*.cxx files.