Add the tree variable goodAdcMult which is the number of raw ADC pulses
  in an ADC channel per event for a given shower array block.

	new file:   Shower2.cxx
	new file:   Shower2.h
	modified:   THcCherenkov.cxx
	modified:   THcCherenkov.h
	modified:   THcShowerArray.h
	modified:   include/HallC_LinkDef.h

Add variable for the difference between the Hodoscope start time
and the ADC pulse time.

Select good adc hit based on window on this difference

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

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

  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

Make matched cluster variables of the array part of calorimeter private.

Initialize fY variable in the THcShowerHit::THcShowerHit default
constructor.

Correct typo in THcShowerArray::Clear, assign -1000 to fMatchClY.

Edit debug output in THcShowerArray::CoarseProcess and remove obsolete
comments THcShowerArray::MatchCluster.

Clear fSizeClustArray and fNblockHighEnergy quantitites in
THcShower::Clear, for just in case.

THcShowerHit.h and THcShowerHit.cxx
---------------
1) Added fY for horizontal position
2) Added fY to THcShowerHit

THcShower.h
-----------
1) Added variables
2) Added method addY, clY to get the cluster Y position

THcShower.cxx
--------------
1) Added variables to the tree for "layer" detector
    either SHMS preshower or HMS layers
2) Added variables if the SHMS "array" is used
3) Added y position to THcShowerHit in CoarseProcess
4) In FineProcess, if SHMS "array" used then fill X,Y info
     for the Cluster and the "best" track that matched the cluster

THcShowerArray.h and THcShowerArray.cxx
---------------------------------------
1) Added methods to Get the array cluster size, X and Y position
   and block number that has the highest energy in the cluster
2) Added array fBlockClusterID for all blocks. initialized to -1
   for each block for each event and then filled with
   the cluster number if the block is included in the cluster
3) Add variable fNhits and fNgoodhits

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...

       This is to match the class name defined in those files
       Also add THcShowerHit to the Makefile

THcShowerHitClass.h file.

fly's eye part.

from SHMS shower counter. Make THcShowerArray a friend class to
THcShower in order to have access to the debug flags.

  Enable by defining HITPIC in THcShowerArray.h

  GetData accepts a pedestal range and an integration range.
  Samples in the integration range are added after subtracting the
  average of the pedestal range from each sample.
  Method also provided to return dynamic pedestal

  Added as an optional sub detector THcShowerArray to the THcShower class
  Get hit data with GetData method instead of hit member variables
    so as to be compatible with FADC compatible hit list