Separate methods for ref time subtracted and raw hits

Update THcHodoScope and THcScintillatorPlane to get focal plane time for each plane

used to determine focal plane time for each hodoscope plane.
Add code to THcScintillatorPlane:DefineVariables to write out
focal plane time, number of paddles hit that passed minimal TDc cut
and number of paddle hit that were used in determining the focal plane time.
Add calls to THcScintillatorPlane.h to Set and Get the focal plane time
and number of paddle hits used to determine focal plane time for each hodoscope plane.

  Nint of an Int gave a compiler error in newer gcc
  Commented out local variables that are not used

  If the podd docs are built using the ROOT tagfile, then when the hcana
  docs are built using the podd tag file, doxygen crashes.  This commit
  adds building of the podd docs to the hcana doc building Makefile.  The
  podd docs are built without using the ROOT tagfile, so a sed hack is used
  to modify podd's Doxyfile.

  Use ROOT's xml layout file
    Customize for hcana, with Hall C logo
  Use tag files from podd and ROOT
  Use groups, starting with a Detector group

  docs/Makefile now builds doxygen docs in docs/html
  If you want documentation to be build elsewhere, define
  DOXYGEN_OUTPUT_DIRECTORY and run doxygen by hand

Doyxgen setup

  Fixed for make and scons
  Put libHallC before libHallA before root libs

  Rename ScalerLoc so it doesn't conflict with class of same name in podd
  Ignore .pcm files
  Makefile does version check for root 6
  Address warnings in hodtest.C

       This is to match the class name defined in those files
       Also add THcShowerHit to the Makefile

    shms-calo-test directory comprises codes for testing. The 1-st
    layer of SOS calorimeter mimicks the SHMS Preshower, and positive
    side of the 2-nd layer mimicks fly's eye part.

THcShowerHitCluster.cxx.