Fix places where the pedestal was set as Integer, so that it is
Double_t everywhere.

In ProcessHits add check of adc in if statements when calculating
the time walk correction.

  Add doxygen groups "Apparatuses" and "Decoders"
  Make sure every class is in a group
  Make sure most classes have a \brief description
  Improve comments for some classes including THcHallCSpectrometer
     and hodoscope classes
  Change some Doxyfile defaults.  Include sources files.

  Set hodoscopes to standard ADC mode for example hodtest.C script
  badcraw_pos and badcraw_neg always true if not Dynamic pedestal mode
  Don't crash in hodoscope if there is no Cherenkov.

Modified Hodoscope and ScintillatorPlane  classes for new time calibration method.

Add AdcTimeWindowMin and Max for each pmt

Add tree variables GoodPosAdcMult and fGoodPosAdcHitUsed

Have variables fGoodPosAdcTdcDiffTime and fGoodNegAdcTdcDiffTime
which are the difference
between TDC time and ADC pulse time

Replace ADC pulse time cut with cut on difference
between TDC time and ADC pulse time to select
good ADC pulse.

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

Fix logical flaw in THcScintillator::ProcessHits in finding good adc hit in multiple hits in one channel

When looping over hits to find the best ADC hit, the code was looping over
frNegAdcPulseInt->GetEntries() or frPosAdcPulseInt->GetEntries()
which are the raw arrays that are filled for all raw hits in the plane
The code was not  using the proper indexes to access the right hits.

The logic is simpler if one loops over rawNegAdcHit.GetNPulses()
or rawPosAdcHit.GetNPulses() which are the the raw hit object for the
paritcular hit. NPulses is the number of ADC pulses that were found for that
adc channel.
The first adc pulse for the channel which is within the adc time window
then has its information saved for late insertion into the "good"
vectors for the hit if either the hit passes 'good" tdc and adc for the POS
or NEG side of the PMT.

    THcHodoscope.cxx
    1. Remove from the use of "temp_planes" for SHMS which
         used only 3 planes for beta and determination of start time.

    2. With change of Integral ADC to pC, change TMath::Sqrt(TMath::Max(20.0,adc_pos))
      to Math::Sqrt(TMath::Max(20.0*.020,adc_pos)) to convert 20 channels to pC

    3. Set fGoodFlags[itrack][ip][iphit].onTrack = kTRUE; when fTOFPInfo[ih].onTrack
       Was always FALSE before.

    4. Modify FineProcess
       a. Add calculation of the track X and Y track position at each plane.
       b. Calculate the difference between the track position and position
          measured by hodoscope center. If multiple paddles hit then take
          average of the paddles.

    THcScintillatorPlane.h and cxx

    1. add variables fHitDistance,fTrackXPosition and fTrackYPosition
    2. add methods GetHitDistance(),GetTrackXPosition(),GetTrackYPosition()
    3. add methods SetHitDistance,SetTrackXPosition,SetTrackYPosition
    4. add variables to tree DiffDisTrack,TrackXPos and TrackYPos
    5. set GoodPosAdcPulseTime to frPosAdcPulseTime
    6. set fGoodNegAdcPulseTime to frNegAdcPulseTime
    7. in HodoHit set PosADCtime and NegADCtime to PulseTime

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

  fpTimes, fScinTime, fScinSigma and fScinZpos are not used.
  These arrays were given fixed size of 53.
  This commit finishes issue #53

Change per event initialization of Good TDC quantities
from zero to kBig.

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

Also do some whitespace cleanup

  This is so that hodoscope paddles in Eve are illuminated

-Changed the name of a Good tdc variables
-Added all good adc and tdc variables
modified:   src/THcScintillatorPlane.cxx
modified:   src/THcScintillatorPlane.h

example:
-fTotNumPosAdcHits (raw hodo+ multiplicity)
-fTotNumNegAdcHits (raw hodo- multiplicity)
-fTotNumAdcHits (raw hodo multiplicity)

Indentation cleanup

   Added to THcScintillatorPlane.h
   Initialize and clear in THcScintillatorPlane.cxx
Add raw multiplicities for ADCs and TDCs

Accidentally deleted line
btdcraw_pos = kTRUE;

in previouse commit

-Added fAdcTimeWindow Min/Max to THcHodoscope.cxx (.h)
-Added fAdcTimeWindow Min/Max to THcScintillatorPlane.cxx (.h)
-Initialized loop over number of hits inside the FillDynamic_Pedestal() method
-added some variables in the THcScintillatorPlane.cxx Dynamic Pedestal Method
-Added loop over adc_pos and adc_neg hits, and required the hits to fall
within fAdcTimeWindow Min/Max
-Added the requirement of at least a valid (adc && tdc) on either end of a bar
-re-defined boolean operator for adc_pos/adc_neg to be True if  they passed the errorflag and timeCUT requirements in the fADC_Dynamic Pedestal method.
-- deleted adc_pos/neg initial definitions, and set their initial values to -999.

Temporarily set THcHodoscope.cxx so that only the first three planes are used to calculate the focal
plane time and beta.
In THcHodoscope , Modified format for writing out the dump file used in hodo calibration.
Add cosmicflag to THcScintillatorPLane so the corrected time is done right for cosmics.
Modified hc_hodo_calib/tofcal.f so that it uses detector 10 as the reference
and that it writes out better defualts for parameters in there are not enough events for a PMT.

THcHodoHit.h add methods to set and get the ADC peak amp and time
THcScintillatorPlane::ProcessHits changed to set the ADC peak amp and time in the Hodohit
DefineVariable added variables to tree

With the new raw and good varibles added to the tree, these variables are not needed in the tree.

The calls to `Find()` need to be wrapped in checks if returned pointer is null.
Otherwise a further call to get value produces SegFault. The `LoadParmValues()`
does not suffer from this, since it throws error if non-optional parameter is
not found. The error message also tells which parameter is missing.

I still left three calls to `Find()` in `THcAnalyzer.cxx`. They are wrapped in
checks and some other things...

Modify default tdc_neg and tdc_pos = -999
SetCorrectedTimes when only oneside has TDC within in window

 - 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 makes the code nicer and with less duplication in logic.

Along with that I had to correct all the call sites to the RawHodoHit in all the
classes that use it.

  Use xhodo_adc_mode to choose how to interpret data
    0 - Interpret as a standard ADC, subtracting pedestal found from ped events
    1 - Use integrated pulse from ADC.  Subtract the event by ev pedestal
    2 - Integrate the sample data, subtract ped found from ped events
    3 - Integrate the sample data, subtract dynamic pedestal
  xhodo_pedestal_scale is factor to multiply dynamic pedestal before
    subtracting.  For example, if uses 4 samples to get pedestal and
    is acquiring 86 samples, in mode 3, this should be 86/4
  xhodo_adc_diag_cut is a cut used to determine if diagnostic ADC
    stuff should be put in tree for each channel.  Need to set this so
    that hodoscope hitmaps get filled right.  Was 50 for Fastbus data.

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