added multiplicity variable to THcShowerPlane.cxx/.h, and fixed multiplicity defined in THcCherenkov.cxx (#372)

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

  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.

  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...

   This is magic that allows the size of arrays to passed to
   the root tree making.

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

Started with Simon's code, but reworked:
	Use podd style arrays in RVarDef.
	Get plane names (1pr, 2ta, 3ta, 4ta) from parameter file.
	Get block counts from parameters instead of hardwiring.
	Rename histogram names to be A,B,C,D 1-13, instead of 1-52

add simple code to register ADC and TDC hits into global
variables so that hit maps can be made.

Add ThcSignalHit class