instead of using GetParent() every hit to get DC version.

Main change was to allow the beam X and Y positions and angle
at the target to be read in through parameters instead of
always using the EPICS data. This gives added flexibility.

If either of the beam position parameters (gbeam_xoff or
gbeam_yoff) are read-in as parameters, then the code uses
the read-in parameters as the BPM position at target. If
there are other beam position or angle parameter that are
not read in then they are set to zero.


1) Modify THcRaster.h
   a) Added variables for X and Y beam angles at target.
   b) Added variable fFlag_use_EPICS_bpm which is a flag
     that is determines whether the code uses the parameters
     or EPICS reads.

2) Modified THcRaster.cxx
   a) set default BPM z-positions to Fall 2018 survey.
   b) Modified Process method so that the BPM position/angle variables
     that are set by parameters are no longer recalculated. Just
     use the existing variables fXbpm_tar, fYbpm_tar, fXpbpm_tar
      and fYPbpm_tar throughout the method.

Add the variable ebeam_epics to the tree. This is the EPICS
value of HALLC:p  . For now this is good for monitoring changes in the
beam energy but needs to be check how it compares to the Hall C
beam energy measurement.

1) THcDCWire.h
  a) added sigma to THcDCWire constructor which fills fSigmaWire
  b) added GetSimga method
  c) added SetSigma method

2) THcDCHit.h
 a) Added GetWireSigma method

3) THcDriftChamberPlane.h
 a) Added flag fUsingSigmaPerWire
 b) Added array fSigmaWire

4) THcDriftChamberPlane.cxx
 a) In ReadDatabase, set fUsingSigmaPerWire=0 by default
    with reading of parameter h_using_sigma_per_wire optional
    for setting fUsingSigmaPerWire.
 b) If fUsingSigmaPerWire=0 then sets all wires in array fSigmaWire to
   fSigma ( which is the simga per plane).
 c) If fUsingSigmaPerWire=1 then reads in the sigma per wire from
   a parameter file.
 d) Used new THcDCWire constructor to set the sigma for wire to fSigmaWire[nwire]
 e) Also change code so that the tzero offset is set in the  THcDCWire constructor
 f) In ProcessHits , use wire->GetTOffSet instead of the fTzeroWire array when setting
    the time.

5) THcDC.cxx
 a) In TrackFit, replace fSigma with hit->GetWireSigma()

1) add variable fHodoEff_CalEnergy_Cut

2) THcHodoEff::ReadDatabase
   Optionally read in parameter hHodoEff_CalEnergy_Cut (HMS) or
        pHodoEff_CalEnergy_Cut (SHMS) and fill fHodoEff_CalEnergy_Cut
   If no parameter then defaults to fHodoEff_CalEnergy_Cut = 0.050

3) fHodoEff_CalEnergy_Cut
    In "if" statements that select events for hodoscope efficiency
    replay hard-coded "0.05" with fHodoEff_CalEnergy_Cut

  Previously, if load was called with a run number, array continuation
  lines in included files were being interpreted as lists of run numbers.
  Still we have the limitation that in the top file, if we define an array
  with multiple lines, the continuation lines will be interpreted as
  run number lists and mess things up.  But it is unlikely that we would
  need to define arrays in the top file when we are in run number
  mode.

Added setting of spectrometer mispointing according the the input
spectrometer angle if the mispointing is not set by a parameter.

The formulas for deteriming the mispointing comes from fits to sureys.

If one wants to use different spectrometer mispointings then
it is best to set hmispointing_x,hmispointing_y for HMS
and pmispointing_x,pmispointing_y for SHMS in the kinematics setting file
such as standard.kinematics .

1) Add tree variables for the three BPMs and projections to target
in the EPICs coordinate system (+X beam right, +Y up)
rb.raster.fr_xbpm_tar
rb.raster.fr_ybpm_tar
rb.raster.fr_xbpmA
rb.raster.fr_ybpmA
rb.raster.fr_xbpmB
rb.raster.fr_ybpmB
rb.raster.fr_xbpmC
rb.raster.fr_ybpmC

2) Modified code so that it only modifies the BPM variables if they
are all !=0 ( beam on) . Otherwise it sets them to the previous EPICS
read. This gets rid of all zero EPICS reads,except if the first EPICs
read the beam is off.

3) Removed the reading of gpbeam from the global parameter list in the Process
  method and just have it in ReadDatabase.

4) Change the calculation of beam at target to use the projection of
   BPM_A and BPM_C instead of BPM_A and BPM_B.

5) Remove setting the raster position to the hcana beam coordinate system
   with (+X beam left). The raster is in the EPICS coordinate system.
    This makes it easier to interpret the carbon hole runs.

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

1) THcExtTarCor.h
   a) add variables fxsieve and fysieve
   b) Added clear method so that fxsieve and fysieve could be set to kBig at start of each event.

2) THcExtTarCor.cxx
   a) Add variables extcor.xsieve and extcor.ysieve to tree
   b) Added clear method.
   c) Added calculation of xsieve and ysieve for golden track. The
      calculation depends on spectrometer. SHMS includes delta dependence
      when calculating ysieve.

Add default values for optional values of
+   fgbpma_zpos = 370.82;
    fgbpmb_zpos = 224.96 ;// cm
    fgbpmc_zpos = 129.30 ;// cm

instead of zero.

Otherwise the code would get NaN for the calculated target beam position
since it was divied by zero unless this the parameters are set.

Modify code in CoarseProcess to add (subtract) time due to hit
location in paddle for positive (negative) PMT for new hodoscope
beta parameters.

Add tree variables TimeHist_Sigma, TimeHist_Peak and TimeHist_Hits
for the peak,sigma and number of hits of the histogram
 of PMT times used in EstimateFocalPlaneTime

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

Handle cases where BPM information is unavailable/zero.

Change raster x/y position calculation to cm (from mm).

Update calculation of fPosition and fDirection in THcRaster.cxx

Fix minor bug in calculation of fDirection

  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.

  Not doing so leads to build error on some systems with cmake.

  Includes THaAnalyzer::GetEpicsEvtHandler and variable vector value helper

  When Load is called with a run number, then the input file is ignored
  until a line with a list of run numbers or run number ranges is found.
  For example:
     44,50-90,113
  If the run number matches one of these run numbers or ranges,
  parameter definitions after the match are loaded.  (Until the next
  list of run numbers and ranges.)
  Before this commit, only a single run number or a single range of
  run numbers was allowed.

  THcTimeSyncEvtHandler can correct runs where the 1190's in a crate
  go out of sync because of a large event.  (This would happen in the
  spring of 2018.  Should be fixed in the DAQ now.)  It a previous version
  this sync problem was detected by looking for 1190 banks that were too large.
  In this update, the first event is used to make a list of which slots
  have TDCs in them.  For subsequent events, it checks that every TDC slot
  has a header and trailer word in the bank.  If any TDCs are found to be
  missing, and the bank size is above a threshold, subsequent events are
  presumed to be out of sync and corrected for in the filtered run output file.

  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.

1. Update for ROOT5-enabled root_generate_dictionary CMake function

  root_generate_dictionary now works with both ROOT 5 and ROOT 6.
  It defines the dictionary custom target and PCM file internally,
  as appropriate, and also automatically extracts any required
  -D compile definitions from the given target(s).

2. Add configuration option HCANA_BUILTIN_PODD (default ON)

  If set to OFF (cmake -DHCANA_BUILTIN_PODD=OFF ...), CMake will find a
  pre-built version of Podd according to the usual find_package search
  rules. (It's sufficient to have the installed "analyzer" in your PATH,
  but you can also set CMAKE_PREFIX_PATH to the Podd installation root,
  for example.) This version of Podd has to have been built and
  installed with Podd's CMake system. In this case, only libHallC will
  be built, and the Podd submodule of hcana is ignored and does not even
  have to be present.

3. Clean existing src/hc_compiledata.h during CMake configuration

  This file might be left over from a previous non-CMake build and would
  be incorrectly picked up instead of the CMake-generated version.

4. Generate hcanaConfig.cmake config and version files using latest Podd scripts

  Requires Podd at commit JeffersonLab/analyzer@34dd368

Requires Podd at commit JeffersonLab/analyzer@aa4c6a8

  Includes experimental cmake build