Added TClonesArray* fRawHits which an array of THcDCHit object for all
hits in the drift chamber. This is filled during Process method.

Added tree variable raw.wirenum whihc is array of wire numbers for all hits in the drift chamber.

  Determine readout side in THcDriftChamberPlane at initialization time.

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()

  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.

Add call ConvertTimeToDist in SubtractStartTime method

THcDriftChamberPlane

  1) Remove subtraction of hodoscope starttime from ProcessHits
    which is called by THcDC::Decode.
  The hodoscope start time is determined in hodoscope Decode
   which is called after THcDC::Decode. So drift chamber
   was using the starttime from the previous event.

   2) Create method SubtractStartTime which is called by THcDC:CoarseTrack

THcDriftChamber
    1) Move fChambers[ic]->ProcessHits() to CoarseTrack
    2) Before looping through fChambers[ic]->ProcessHits() in CoarseTrack
        loop through all planes and call fPlanes[ip]->SubtractStartTime()

Add rawnorefcorrtime to THcDCHit which is the TDC raw without
the reference time subtraction.

Add variable rawnorefcorrtdc in THcDriftChamberPlane::DefineVariables

Modify THcDriftChamberPlane::ProcessHits to call GetRawTdcHit().GetTimeRaw
  and call THcDCHit with new extra argument for raw time without reference time
  subtraction.

1) Add X,Y offsets parameter for each plane, instead of X,Y offset per chamber
2) ModifyTHcDriftChamber::CorrectHitTimes to work with SHMS chambers
3) Add GetReadoutSide method to THcDCHit class.

Main purpose is to calculate the DC efficiency per wire
using the track information of the golden track.


THcDC.h
-----------
1) add method EfficiciencyPerWire
2) Add variables fWire_hit_did and fWire_hit_should

THcDC.cxx
------------
1) fWire_hit_did and fWire_hit_should are fixed length arrays
   the size of NPlanes that in set in method Init
2) Add variables wireHitDid and wireHitShould to the tree
3) In method SetFocalPlaneBestTrack add call to EfficiencyPerWire method
4) added EfficiencyPerWire method which loops over the hits
    and compares the wire number for the hit to the the track
    position at the plane (convert back to wire number).
    Then fills fWire_hit_did with the wire number if
    equal to the wire position of the hit equals the track.
    Also does loop over all planes and fills fWire_hit_should
    with the wire number of the track in each plane.

THcDriftChamberPlane.h and cxx
---------------------
1) Added method CalcWireFromPos

Main purpose was to have option for per wire tzero offsets

Modified THcDriftChamberPlane.h
------------------------------
1) added fUsingTzeroPerWire as parameter flag to switch on per wire tzero offsets when parameter equals 1
2) fTzeroWire is array of tzero offsets for each wire in plane

Modified THcDriftChamberPlane.cxx
------------------------------
1) THcDriftChamberPlane::ReadDatabase
    a)set a default value of fUsingTzeroPerWire=0
    b)added to DBRequest list option to read in fUsingTzeroPerWire
    c) if fUsingTzeroPerWire=1 then separate DBRequest to read in fTzeroWire
   d) if fUsingTzeroPerWire=0 then all fTzeroWire=0

2) THcDriftChamberPlane::ProcessHits
------------------------------------
   a) Modify calcualation of drift time to subtract fTzeroWire
Double_t time = -StartTime- rawtdc*fNSperChan + fPlaneTimeZero - fTzeroWire[wireNum-1];

Applied changes in several files to reflect this.
Minor fix in `THcRawHodoHit`.

in THcDrifthChamberPlane::DefineVariable and output.def

  Separate methods for ref time subtracted and raw hits

  Base class THcRawHit has null GetReference method.  Returns
  zero.
  THcRawDCHit will get the reference time if it was specified in the map file.
  It is up to the detector class to use the reference time to subtract off
  pipeline TDC jitter.

  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

  For the most part this is making sure that the loop variable in
  a for loop is of the same type as the variable that it is compared
  against (Often a UInt_t).

This reverts commit e9ce1040.

Conflicts:
	src/THcHallCSpectrometer.cxx

  For the most part this is making sure that the loop variable in
  a for loop is of the same type as the variable that it is compared
  against (Often a UInt_t).

In tree they are called tnhit and trawhit.
Created two new variables for THcDriftChamber, fNthits and fN_True_RawHits.
In tree they are called tnhit and trawhit.
THcDC defined subdetector THcDriftChamber to have name Ch1 and Ch2 to do used in the tree.
THcDriftChamberPlane defined new method GetNRawhits to return fNRawhits for each plane.
Added member fNRawhits to THcDriftChamberPlane

These were related to a) scope of some variable declarations, and b) use
of pre-increment vs. post-increment of non-primitive types (this has a
slight performance hit due to the way that pre- vs. post-increment
operators are overloaded in C++.

Also cleaned up a few places where initialized variables were not being
used.

  Clone some DC tests from ENGINE test files to podd
  style cuts.  Make changes to source code to support these tests.
  Correct hits in plane line in example report file.

  Uses ROOT matrix math instead of solve_four_by_four
  Nothing is done with found tracks yet.  Will need to stuff these into
     podd style tracks.  (Or a class inherited from podd style tracks.)
  Residuals not saved anywhere
  Single stub mode not yet implemented
  No printing out of trackfit results (hdebugtrackprint)

  Compiles and doesn't crash.

  THcDriftChamber::SpacePoint -> THcSpacePoint
  That way space points can be put in a TClonesArray and be made known
  to THcDC when stub information is added.