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.

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

  Don't check if UInt_t's are >=0
  Remove unused/repeated variables
  Cast enums to Int_t in switch statements
  Initialize temp variables

- Added range checks when adding data to hits. Now an error
is thrown instead of potentially getting core dump.

  (Assignment probably not actually done with these objects,
  so we might want to remove these methods.)

  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.

  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).

      Start adding to the drift chamber code.   Setup a class structure
      similar to what podd uses for the VDCs.  Raw hit class renamed
      to THcRawDCHit.  Signal hits are how THcDCHit, modeled after
      podd hits.  Add THcDCWire, and classes for time to distance conversion.
      Time to distnace conversion doesn't do anything yet.

      Find some improved DC parameter files so that min and max TDC limits
      are good for the run we are using.

      THcDriftChamberPlane asks ThcDriftChamber for many parameters.

TClonesArray ConstructedAt method.

Raw hit class for drift chambers and skeleton drift chamber that prints
out drift chamber package hits.

Move Compare method from THcHodoscopeHit to ThcRawHit since it should
work for any derived class.

Get detector name -> ID mapping from the map file comments