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.

  Other missing energy def name changed to emiss_nuc
  Get secondary particle mass from the parameter DB
    instead of the spectrometer object

**This class calculates kinematic variables related to the secondary (hadron)
detected particle