diff --git a/SConstruct b/SConstruct
deleted file mode 120000
index 0fe1cae2e2aaa80a9dbba1a7c62ed71003c29aeb..0000000000000000000000000000000000000000
--- a/SConstruct
+++ /dev/null
@@ -1 +0,0 @@
-SConstruct.py
\ No newline at end of file
diff --git a/SConstruct b/SConstruct
new file mode 100644
index 0000000000000000000000000000000000000000..6d89421a9253a794b3dfcaaca6f1cac10d911a52
--- /dev/null
+++ b/SConstruct
@@ -0,0 +1,167 @@
+###### Hall C Software Main SConstruct Build File #####
+###### Author:	Edward Brash (brash@jlab.org) June 2013
+
+import os
+import sys
+import platform
+import commands
+import SCons
+
+def rootcint(target,source,env):
+	"""Executes the ROOT dictionary generator over a list of headers."""
+	dictname = target[0]
+	headers = ""
+	cpppath = env.subst('$_CCCOMCOM')
+	ccflags = env.subst('$CCFLAGS')
+	rootcint = env.subst('$ROOTCINT')
+	print "Doing rootcint call now ..."
+	for f in source:
+		headers += str(f) + " "
+	command = rootcint + " -f %s -c -pthread -fPIC %s %s" % (dictname,cpppath,headers)
+	print ('RootCint Command = %s\n' % command)
+	ok = os.system(command)
+	return ok
+
+baseenv = Environment(ENV = os.environ)
+#dict = baseenv.Dictionary()
+#keys = dict.keys()
+#keys.sort()
+#for key in keys:
+#	print "Construction variable = '%s', value = '%s'" % (key, dict[key])
+
+####### Check SCons version ##################
+print('!!! Building the Hall C analyzer and libraries with SCons requires')
+print('!!! SCons version 2.1.0 or newer.')
+EnsureSConsVersion(2,1,0)
+
+####### Hall A Build Environment #############
+#
+baseenv.Append(MAIN_DIR= Dir('.').abspath)
+baseenv.Append(HC_DIR= baseenv.subst('$MAIN_DIR'))
+baseenv.Append(HC_SRC= baseenv.subst('$HC_DIR')+'/src ') 
+baseenv.Append(HA_DIR= baseenv.subst('$HC_DIR')+'/podd ')
+baseenv.Append(HA_SRC= baseenv.subst('$HA_DIR')+'/src ') 
+baseenv.Append(HA_DC= baseenv.subst('$HA_DIR')+'/hana_decode ') 
+baseenv.Append(HA_SCALER= baseenv.subst('$HA_DIR')+'/hana_scaler ') 
+baseenv.Append(MAJORVERSION = '1')
+baseenv.Append(MINORVERSION = '5')
+baseenv.Append(PATCH = '25')
+baseenv.Append(SOVERSION = baseenv.subst('$MAJORVERSION')+'.'+baseenv.subst('$MINORVERSION'))
+baseenv.Append(VERSION = baseenv.subst('$SOVERSION')+'.'+baseenv.subst('$PATCH'))
+baseenv.Append(EXTVERS = '')
+baseenv.Append(HA_VERSION = baseenv.subst('$VERSION')+baseenv.subst('$EXTVERS'))
+print "Hall C Main Directory = %s" % baseenv.subst('$HC_DIR')
+print "Hall C Source Directory = %s" % baseenv.subst('$HC_SRC')
+print "Hall A Main Directory = %s" % baseenv.subst('$HA_DIR')
+print "Software Version = %s" % baseenv.subst('$VERSION')
+ivercode = 65536*int(float(baseenv.subst('$SOVERSION')))+ 256*int(10*(float(baseenv.subst('$SOVERSION'))-int(float(baseenv.subst('$SOVERSION')))))+ int(float(baseenv.subst('$PATCH')))
+baseenv.Append(VERCODE = ivercode)
+baseenv.Append(CPPPATH = ['$HC_SRC','$HA_SRC','$HA_DC','$HA_SCALER'])
+
+proceed = "1" or "y" or "yes" or "Yes" or "Y"
+######## Configure Section #######
+
+import configure
+configure.config(baseenv,ARGUMENTS)
+
+Export('baseenv')
+
+conf = Configure(baseenv)
+
+if not conf.CheckCXX():
+	print('!!! Your compiler and/or environment is not correctly configured.')
+	Exit(0)
+
+if not conf.CheckFunc('printf'):
+       	print('!! Your compiler and/or environment is not correctly configured.')
+       	Exit(0)
+
+if baseenv.subst('$CHECKHEADERS')==proceed:
+	system_header_list = ['arpa/inet.h','errno.h','assert.h','netdb.h','netinet/in.h','pthread.h','signal.h','stddef.h','stdio.h','stdlib.h','string.h','strings.h','sys/ioctl.h','sys/socket.h','sys/time.h','sys/types.h','time.h','unistd.h','memory.h','math.h','limits.h']
+
+	for header_file in system_header_list:
+		if not conf.CheckHeader(header_file):
+			print('!! Header file %s not found.' % header_file)
+			Exit(0)
+
+baseenv = conf.Finish()
+
+######## ROOT Dictionaries #########
+baseenv.Append(ROOTCONFIG = 'root-config')
+baseenv.Append(ROOTCINT = 'rootcint')
+
+try:
+        baseenv.ParseConfig('$ROOTCONFIG --cflags')
+        baseenv.ParseConfig('$ROOTCONFIG --libs')
+        baseenv.MergeFlags('-fPIC')
+except OSError:
+        try:
+		baseenv.Replace(ROOTCONFIG = baseenv['ENV']['ROOTSYS'] + '/bin/root-config')
+		baseenv.Replace(ROOTCINT = baseenv['ENV']['ROOTSYS'] + '/bin/rootcint')
+		baseenv.ParseConfig('$ROOTCONFIG --cflags')
+		baseenv.ParseConfig('$ROOTCONFIG --libs')
+		baseenv.MergeFlags('-fPIC')
+	except KeyError:
+                print('!!! Cannot find ROOT.  Check if root-config is in your PATH.')
+                Exit(1)
+
+bld = Builder(action=rootcint)
+baseenv.Append(BUILDERS = {'RootCint': bld})
+
+######## cppcheck ###########################
+
+def which(program):
+	import os
+	def is_exe(fpath):
+		return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
+	
+	fpath, fname = os.path.split(program)
+	if fpath:
+		if is_exe(program):
+			return program
+	else:
+		for path in os.environ["PATH"].split(os.pathsep):
+			path = path.strip('"')
+			exe_file = os.path.join(path, program)
+			if is_exe(exe_file):
+				return exe_file
+	return None
+
+if baseenv.subst('$CPPCHECK')==proceed:
+	is_cppcheck = which('cppcheck')
+	print "Path to cppcheck is %s\n" % is_cppcheck
+
+	if(is_cppcheck == None):
+		print('!!! cppcheck not found on this system.  Check if cppcheck is installed and in your PATH.')
+		Exit(1)
+	else:
+		cppcheck_command = baseenv.Command('cppcheck_report.txt',[],"cppcheck --quiet --enable=all src/ 2> $TARGET")
+		baseenv.AlwaysBuild(cppcheck_command)
+
+####### Start of main SConstruct ############
+
+hallclib = 'HallC'
+hallalib = 'HallA'
+dclib = 'dc'
+scalerlib = 'scaler'
+
+baseenv.Append(LIBPATH=['$HC_DIR','$HA_DIR','$HC_SRC','$HA_SRC','$HA_DC','$HA_SCALER'])
+baseenv.Replace(SHLIBSUFFIX = '.so')
+baseenv.Append(CPPDEFINES = '-DHALLC_MODS')
+
+directorylist = ['./','src','podd','podd/src','podd/hana_decode','podd/hana_scaler']
+
+baseenv.Append(SHLIBSUFFIX ='.'+baseenv.subst('$VERSION'))
+pbaseenv=baseenv.Clone()
+pbaseenv.Append(LIBS=[hallclib,hallalib,dclib,scalerlib])
+baseenv.Append(LIBS=[hallalib,dclib,scalerlib])
+Export('pbaseenv')
+
+#SConscript('podd/SConscript.py',exports='baseenv')
+#SConscript('podd/hana_scaler/SConscript.py',exports='baseenv')
+#SConscript('podd/hana_decode/SConscript.py',exports='baseenv')
+#SConscript('src/SConscript.py',exports='baseenv')
+#SConscript('./SConscript.py',exports='baseenv')
+SConscript(dirs = directorylist,name='SConscript.py',exports='baseenv')
+
+#######  End of SConstruct #########
diff --git a/examples/PARAM/52949/hcana.param b/examples/PARAM/52949/hcana.param
deleted file mode 120000
index 7fd888b6ebf1fb22416f5b98f23bbabf7f0d745c..0000000000000000000000000000000000000000
--- a/examples/PARAM/52949/hcana.param
+++ /dev/null
@@ -1 +0,0 @@
-../hcana.param
\ No newline at end of file
diff --git a/examples/PARAM/52949/hcana.param b/examples/PARAM/52949/hcana.param
new file mode 100644
index 0000000000000000000000000000000000000000..47b4766b5526cbf1fd9f0da9393347d6fe98188a
--- /dev/null
+++ b/examples/PARAM/52949/hcana.param
@@ -0,0 +1,79 @@
+;
+; Parameters that were built into Fortran analyzer that we want
+; to pass as parameters so that the resulting code can be more generic.
+;
+
+hhodo_num_planes = 4
+hhodo_plane_names = "1x 1y 2x 2y"
+
+hcal_num_layers = 4
+
+# Exclusion band width for the calorimeter's fiducial volume.
+hcal_fv_delta = 5.
+
+# Constants for the coordiante correction of the calorimeter energy depositions
+hcal_a_cor = 200.
+hcal_b_cor = 8000.
+hcal_c_cor = 64.36
+hcal_d_cor = 1.66
+
+hcal_layer_names = "1pr 2ta 3ta 4ta"
+
+haero_num_pairs = 8
+
+# Names of planes so that parameter names can be constructed
+hdc_plane_names = "1x1 1y1 1u1 1v1 1y2 1x2 2x1 2y1 2u1 2v1 2y2 2x2"
+
+# The following were defined in REPLAY.PARAM
+h_recon_coeff_filename =    'PARAM/hms_recon_coeff.dat'  ;hms optics matrix
+
+# The following are set to zero to replicate historical ENGINE behavior
+# For new analyses they should be set to 1.  If not defined here,
+# hcana will default 1, the new and correct behaviour.
+
+# If 1, Let a hit have different L/R assignment for different space points
+# instead of L/R assignment from first sp it appears in.
+hdc_fix_lr = 0
+# If 1, don't do the the propagation along the wire each time the hit
+# appears in a space point.  (Which means the correction accumulates)
+hdc_fix_propcorr = 0
+
+# SOS parameters
+shodo_num_planes = 4
+shodo_plane_names = "1x 1y 2x 2y"
+
+scal_num_layers = 4
+
+# Exclusion band width for the calorimeter's fiducial volume.
+# (saw) Don't know what this should be.  Copied it from HMS.
+scal_fv_delta = 5.
+
+# Constants for the coordiante correction of the calorimeter energy depositions
+# (saw) Copied from HMS
+scal_a_cor = 200.
+scal_b_cor = 8000.
+scal_c_cor = 64.36
+scal_d_cor = 1.66
+
+scal_layer_names = "1pr 2ta 3ta 4ta"
+
+# Names of planes so that parameter names can be constructed
+sdc_plane_names = "1u1 1u2 1x1 1x2 1v1 1v2 2u1 2u2 2x1 2x2 2v1 2v2"
+
+# The following were defined in REPLAY.PARAM
+s_recon_coeff_filename =    'PARAM/sos_recon_coeff.dat'  ;sos optics matrix
+
+# Fortran ENGINE only had this as a parameter for HMS.  Need it here
+# because same code used for both spectrometers
+sntracks_max_fp = 10
+
+# The following are set to zero to replicate historical ENGINE behavior
+# For new analyses they should be set to 1.  If not defined here,
+# hcana will default 1, the new and correct behaviour.
+
+# If 1, Let a hit have different L/R assignment for different space points
+# instead of L/R assignment from first sp it appears in.
+sdc_fix_lr = 0
+# If 1, don't do the the propagation along the wire each time the hit
+# appears in a space point.  (Which means the correction accumulates)
+sdc_fix_propcorr = 0
diff --git a/src/THcAerogel.cxx b/src/THcAerogel.cxx
index 60f92df71cdd542ce9652b29b1cad7329a510012..8d5e47b6672a4693fe11cfb07256e0d4ae7fe2ca 100644
--- a/src/THcAerogel.cxx
+++ b/src/THcAerogel.cxx
@@ -80,7 +80,7 @@ THaAnalysisObject::EStatus THcAerogel::Init( const TDatime& date )
 
   // Should probably put this in ReadDatabase as we will know the
   // maximum number of hits after setting up the detector map
-  THcHitList::InitHitList(fDetMap, "THcAerogelHit", 100);
+  InitHitList(fDetMap, "THcAerogelHit", 100);
 
   EStatus status;
   if( (status = THaNonTrackingDetector::Init( date )) )
@@ -237,7 +237,7 @@ void THcAerogel::Clear(Option_t* opt)
 Int_t THcAerogel::Decode( const THaEvData& evdata )
 {
   // Get the Hall C style hitlist (fRawHitList) for this event
-  fNhits = THcHitList::DecodeToHitList(evdata);
+  fNhits = DecodeToHitList(evdata);
 
   if(gHaCuts->Result("Pedestal_event")) {
 
diff --git a/src/THcAerogelHit.h b/src/THcAerogelHit.h
index 0c8ac63327be3dcfbcbe809f055da216e86c0b0d..49ddd246adb84eecf18c6214fb2e12e05bb2026d 100644
--- a/src/THcAerogelHit.h
+++ b/src/THcAerogelHit.h
@@ -6,12 +6,13 @@
 class THcAerogelHit : public THcHodoscopeHit {
 
  public:
+  friend class THcAerogel;
  
  protected:
 
  private:
 
-  ClassDef(THcAerogelHit,0);	// Aerogel hit class
+  ClassDef(THcAerogelHit,0);	// Raw Aerogel hit
 };
 
 #endif
diff --git a/src/THcAnalyzer.cxx b/src/THcAnalyzer.cxx
index 6c97bba481b5793e99d0a1a9568d61d7053fee0e..6d3f0c9fd92b9d609b5c47cc239b4ea7d5708b0c 100644
--- a/src/THcAnalyzer.cxx
+++ b/src/THcAnalyzer.cxx
@@ -61,8 +61,10 @@ THcAnalyzer::~THcAnalyzer()
 //_____________________________________________________________________________
 void THcAnalyzer::PrintReport(const char* templatefile, const char* ofile)
 {
-  // Copy template to ofile, replacing {stuff} with the evaluated
-  // value of stuff.
+  // Generate "reports" such as end of run scaler/efficiency sheets
+  // Reads a template file, copying that file to the output, replacing
+  // variables and expressions inside of braces ({}) with evaluated values.
+  // Similar but not identical to ENGINE/CTP report templates.
   ifstream ifile;
   ifile.open(templatefile);
 
@@ -139,9 +141,12 @@ void THcAnalyzer::PrintReport(const char* templatefile, const char* ofile)
 //_____________________________________________________________________________
 void THcAnalyzer::LoadInfo()
 {
-  // Copy some run information into gHcParms variables so that in can
-  // be used in reports.
-  // For example run number, first event analyzed, number of events, etc.
+  // Create several THcParms variables in gHcParms containing 
+  // run information such as
+  // run number, first event analyzed, number of events, etc.
+  //    gen_run_number - Current run
+  //    gen_run_starting_event - Id of first event analyzed
+  //    gen_event_id_number - Id of last event analyzed
   Int_t* runnum;
   Int_t* firstevent;
   Int_t* lastevent;
diff --git a/src/THcCherenkov.cxx b/src/THcCherenkov.cxx
index 2db648b6e83b1100106b6bcb58ce88916bf1188c..5587a54c3a50baaa1a4e345c350cea433e37cb35 100644
--- a/src/THcCherenkov.cxx
+++ b/src/THcCherenkov.cxx
@@ -95,7 +95,7 @@ THaAnalysisObject::EStatus THcCherenkov::Init( const TDatime& date )
 
   // Should probably put this in ReadDatabase as we will know the
   // maximum number of hits after setting up the detector map
-  THcHitList::InitHitList(fDetMap, "THcCherenkovHit", 100); // 100 is max hits
+  InitHitList(fDetMap, "THcCherenkovHit", 100); // 100 is max hits
 
   EStatus status;
   if( (status = THaNonTrackingDetector::Init( date )) )
@@ -206,7 +206,7 @@ void THcCherenkov::Clear(Option_t* opt)
 Int_t THcCherenkov::Decode( const THaEvData& evdata )
 {
   // Get the Hall C style hitlist (fRawHitList) for this event
-  fNhits = THcHitList::DecodeToHitList(evdata);
+  fNhits = DecodeToHitList(evdata);
 
   if(gHaCuts->Result("Pedestal_event")) {
 
diff --git a/src/THcCherenkovHit.h b/src/THcCherenkovHit.h
index 67ef4c13c1e0a344a06803a581d81b869d79e426..63a0aab95b7faf61220b5709bfc5d50f7eed1919 100644
--- a/src/THcCherenkovHit.h
+++ b/src/THcCherenkovHit.h
@@ -6,12 +6,13 @@
 class THcCherenkovHit : public THcHodoscopeHit {
 
  public:
+  friend class THcCherenkov;
  
  protected:
 
  private:
 
-  ClassDef(THcCherenkovHit,0);	// Cherenkov hit class
+  ClassDef(THcCherenkovHit,0);	// Raw Cherenkov hit
 };
 
 #endif
diff --git a/src/THcDC.cxx b/src/THcDC.cxx
index be89cfc5f2c3f65137b51c0336d7a99c5b06a37e..63199d525b6b534a8fafb6e4f1531ff6931fdd15 100644
--- a/src/THcDC.cxx
+++ b/src/THcDC.cxx
@@ -170,7 +170,7 @@ THaAnalysisObject::EStatus THcDC::Init( const TDatime& date )
 
   // Should probably put this in ReadDatabase as we will know the
   // maximum number of hits after setting up the detector map
-  THcHitList::InitHitList(fDetMap, "THcRawDCHit", 1000);
+  InitHitList(fDetMap, "THcRawDCHit", 1000);
 
   EStatus status;
   // This triggers call of ReadDatabase and DefineVariables
@@ -427,7 +427,7 @@ Int_t THcDC::Decode( const THaEvData& evdata )
   Int_t num_event = evdata.GetEvNum();
   if (fdebugprintrawdc ||fdebugprintdecodeddc || fdebuglinkstubs || fdebugtrackprint) cout << " event num = " << num_event << endl;
   // Get the Hall C style hitlist (fRawHitList) for this event
-  fNhits = THcHitList::DecodeToHitList(evdata);
+  fNhits = DecodeToHitList(evdata);
 
   // Let each plane get its hits
   Int_t nexthit = 0;
@@ -1017,6 +1017,7 @@ Double_t THcDC::DpsiFun(Double_t ray[4], Int_t plane)
 Int_t THcDC::End(THaRunBase* run)
 {
   //  EffCalc();
+  return 0;
 }
 
 //_____________________________________________________________________________
diff --git a/src/THcDC.h b/src/THcDC.h
index 68ea8072538fb3fa7112d25aac64a30987c23bfc..05d5def06181cd6bed17bdba9c9716f418e0e693 100644
--- a/src/THcDC.h
+++ b/src/THcDC.h
@@ -173,7 +173,7 @@ protected:
   void Setup(const char* name, const char* description);
   void PrintSpacePoints();
 
-  ClassDef(THcDC,0)   // Drift Chamber class
+  ClassDef(THcDC,0)   // Set of Drift Chambers detector
 };
 
 ////////////////////////////////////////////////////////////////////////////////
diff --git a/src/THcDCHit.h b/src/THcDCHit.h
index 80302bd549954fb18dd65c1dd315d0b6ffcef71b..c5ca7a74d3e14038ab2fc037cfd7bc31be6adee5 100644
--- a/src/THcDCHit.h
+++ b/src/THcDCHit.h
@@ -78,7 +78,7 @@ private:
   THcDCHit( const THcDCHit& );
   THcDCHit& operator=( const THcDCHit& );
   
-  ClassDef(THcDCHit,2)             // VDCHit class
+  ClassDef(THcDCHit,2)             // Drift Chamber Hit
 };
 
 ////////////////////////////////////////////////////////////////////////////////
diff --git a/src/THcDCLookupTTDConv.h b/src/THcDCLookupTTDConv.h
index e1bbea121d91a039e4b477ceabc0c75895bc438e..3d6157436ddca4ab5150af81744fa6e831ef7b23 100644
--- a/src/THcDCLookupTTDConv.h
+++ b/src/THcDCLookupTTDConv.h
@@ -29,7 +29,7 @@ protected:
   Int_t fNumBins;
   Double_t* fTable;
 
-  ClassDef(THcDCLookupTTDConv,0)             // VDC Analytic TTD Conv class
+  ClassDef(THcDCLookupTTDConv,0)             // Time to Distance conversion lookup
 };
 
 
diff --git a/src/THcDCTimeToDistConv.h b/src/THcDCTimeToDistConv.h
index 960a5c373c8396a57c593c8657df78430d70bc2d..2ff706206455a2e40d4ed6b8cfa574fc1145b800 100644
--- a/src/THcDCTimeToDistConv.h
+++ b/src/THcDCTimeToDistConv.h
@@ -24,7 +24,7 @@ private:
   THcDCTimeToDistConv( const THcDCTimeToDistConv& );
   THcDCTimeToDistConv& operator=( const THcDCTimeToDistConv& );
 
-  ClassDef(THcDCTimeToDistConv,0)             // DCTimeToDistConv class
+  ClassDef(THcDCTimeToDistConv,0)             // Time to Distance conversion base class
 };
 
 ////////////////////////////////////////////////////////////////////////////////
diff --git a/src/THcDCTrack.h b/src/THcDCTrack.h
index a9b84c6fbf4ee6ab8392baf357fbfdd44e2cd81f..cc97ff1c03c7e924bef06e537b78be51417e3c43 100644
--- a/src/THcDCTrack.h
+++ b/src/THcDCTrack.h
@@ -85,6 +85,6 @@ private:
   THcDCTrack( const THcDCTrack& );
   THcDCTrack& operator=( const THcDCTrack& );
 
-  ClassDef(THcDCTrack,0)	// DCTrack class
+  ClassDef(THcDCTrack,0)	// Full Drift Chamber track
 };
 #endif
diff --git a/src/THcDCWire.h b/src/THcDCWire.h
index 0e3ce6dce6122392e1e54f4e965b7b797861b529..53f6fcbe39e317c450dfb8440b59c72cfd14c027 100644
--- a/src/THcDCWire.h
+++ b/src/THcDCWire.h
@@ -43,7 +43,7 @@ private:
   THcDCWire( const THcDCWire& );
   THcDCWire& operator=( const THcDCWire& );
  
-  ClassDef(THcDCWire,0)             // VDCWire class
+  ClassDef(THcDCWire,0)             // Drift Chamber Wire class
 };
 
 ////////////////////////////////////////////////////////////////////////////////
diff --git a/src/THcDetectorMap.cxx b/src/THcDetectorMap.cxx
index 187c465db60946ed96919af5618a3ad64b04bf61..a4ff120c9cc6dfe477596163af65859494b52acd 100644
--- a/src/THcDetectorMap.cxx
+++ b/src/THcDetectorMap.cxx
@@ -4,12 +4,8 @@
 //
 // THcDetectorMap
 //
-// Class to read and hold Hall C style detector map
-//
-// Will need method to retrieve all map entries for a given
-// detector id.
-//
-// Not sure we will keep this class, but still need the parsing of the map file
+// Class to read and Hall C style detector map
+//   FillMap method builds a map for a specific detector
 //
 //////////////////////////////////////////////////////////////////////////
 
@@ -54,8 +50,11 @@ struct Functor
 };
 //_____________________________________________________________________________
 Int_t THcDetectorMap::FillMap(THaDetMap *detmap, const char *detectorname)
-// Should probably return a status
 {
+  // Build a DAQ hardware to detector element map for detector detectorname
+  // Reads through the entire list of mappings, adding one element to
+  // detmap for each electronics channel that maps to detectorname.
+
   list<ModChanList>::iterator imod;
   list<ChaninMod>::iterator ichan;
   ChaninMod Achan;
@@ -171,8 +170,35 @@ Int_t THcDetectorMap::FillMap(THaDetMap *detmap, const char *detectorname)
   return(0);
 }
 
+//_____________________________________________________________________________
 void THcDetectorMap::Load(const char *fname)
 {
+// Load a Hall C ENGINE style detector map file.  The map file maps
+// a given roc, slot/module, and channel # into a given detector id#, plane
+// number, counter number and signal type.  The mapping between detector
+// names and ids is found in the comments at the begging of the map file.
+// This method looks for those comments, of the form:
+//   XXX_ID = n
+// to establish that mapping between detector name and detector ID.
+//
+// Lines of the form
+//  DETECTOR = n  
+//  ROC = n
+//  SLOT = n
+// are used to establish the module (roc and slot) and the detector
+// for the mapping lines that follow.
+// The actual mappings are of the form 
+//  subadd, plane, counter [, signal]
+// Each of these lines, combined with the detector, roc, slot values
+// establish the roc, slot, subadess -> detector, plane, counter#, sigtype map
+// Other lines that may be in the map file are
+//  NSUBADD = n
+//  BSUB = n
+//  MASK = hex value
+// These define characteristics of the electronics module (# channels,
+//  The bit number specifying the location of the subaddress in a data word
+//  and hex mask that the data word is anded with to retrieve data)
+
   static const char* const whtspc = " \t";
 
   ifstream ifile;
diff --git a/src/THcDetectorMap.h b/src/THcDetectorMap.h
index 1dd95b2471267ffd7dee8ef096caf6e381b2091b..420f7de84400227c5352079a1a88d4b938e5d8de 100644
--- a/src/THcDetectorMap.h
+++ b/src/THcDetectorMap.h
@@ -60,7 +60,7 @@ class THcDetectorMap : public TObject {
 
  protected:
 
-  ClassDef(THcDetectorMap,0);
+  ClassDef(THcDetectorMap,0); // Map electronics channels to Detector, Plane, Counter, Signal
 };
 #endif
 
diff --git a/src/THcDriftChamber.cxx b/src/THcDriftChamber.cxx
index 69f0c75cbded9475653eec9b4958d992a1d834e5..9d7f93612fcd16844da7d837cf9eca983230b6ec 100644
--- a/src/THcDriftChamber.cxx
+++ b/src/THcDriftChamber.cxx
@@ -309,7 +309,8 @@ Int_t THcDriftChamber::FindSpacePoints( void )
       if(fHMSStyleChambers) {
 	if(fRemove_Sppt_If_One_YPlane == 1) {
 	  // The routine is specific to HMS
-	  Int_t ndest=DestroyPoorSpacePoints(); // Only for HMS?
+	  //Int_t ndest=
+	    DestroyPoorSpacePoints(); // Only for HMS?
 	  // Loop over space points and remove those with less than 4 planes
 	  // hit and missing hits in Y,Y' planes
 	}
@@ -855,7 +856,7 @@ void THcDriftChamber::ChooseSingleHit()
     // Gather the remaining hits
     Int_t finalnum = 0;
     for(Int_t ihit=0;ihit<startnum;ihit++) {
-	THcDCHit* hit = sp->GetHit(ihit);
+      //THcDCHit* hit = sp->GetHit(ihit);
 	//	if (fhdebugflagpr) cout << " good hit = "<< ihit << " " << goodhit[ihit] << " time = " << hit->GetTime() << endl;
       if(goodhit[ihit] > 0) {	// Keep this hit
 	if (ihit > finalnum) {	// Move hit 
@@ -910,7 +911,7 @@ void THcDriftChamber::SelectSpacePoints()
     //if (fhdebugflagpr) cout << " sp pt = " << isp+1 << " # of hits = " << sp->GetNHits() << endl;
     for(Int_t ihit=0;ihit<sp->GetNHits();ihit++) {
       THcDCHit* hit = sp->GetHit(ihit);
-      THcDriftChamberPlane* plane=hit->GetWirePlane();
+      //THcDriftChamberPlane* plane=hit->GetWirePlane();
       //        if (fhdebugflagpr) cout << ihit+1 << "selecting " << plane->GetPlaneNum() << " " << plane->GetChamberNum() << " " << hit->GetTime() << " " << hit->GetDist() << " " << plane->GetCentralTime() << " " << plane->GetDriftTimeSign() << endl;
     }
   }
diff --git a/src/THcDriftChamber.h b/src/THcDriftChamber.h
index b77fca45ed75f682d81e0de0737e9201216f16b1..a7884461cb2e337027420deb215fc2692d7c8f77 100644
--- a/src/THcDriftChamber.h
+++ b/src/THcDriftChamber.h
@@ -134,7 +134,7 @@ protected:
   Double_t* stubcoef[4]; 
   std::map<int,TMatrixD*> fAA3Inv;
 
-  ClassDef(THcDriftChamber,0)   // Drift Chamber class
+  ClassDef(THcDriftChamber,0)   // A single drift chamber
 };
 
 ////////////////////////////////////////////////////////////////////////////////
diff --git a/src/THcDriftChamberPlane.h b/src/THcDriftChamberPlane.h
index d6aa10c896ab37b1bb7349a8deeab219c3ffd4ea..b7aac91b7f1b5b9f18b2ca562b8dc91a0cac3cb0 100644
--- a/src/THcDriftChamberPlane.h
+++ b/src/THcDriftChamberPlane.h
@@ -109,7 +109,7 @@ protected:
 
   THcHodoscope* fglHod;		// Hodoscope to get start time
 
-  ClassDef(THcDriftChamberPlane,0)
+  ClassDef(THcDriftChamberPlane,0); // A single plane within a THcDriftChamber
 };
 #endif
 
diff --git a/src/THcHallCSpectrometer.h b/src/THcHallCSpectrometer.h
index 19826c076097e3aef7867211e542c3c3aa2cc18c..f906546ec9c187e94ec3f607d90b2089420ae0ad 100644
--- a/src/THcHallCSpectrometer.h
+++ b/src/THcHallCSpectrometer.h
@@ -57,7 +57,7 @@ protected:
   // Flag for fProperties indicating that tracks are to be sorted by chi2
   static const UInt_t kSortTracks = BIT(16);
 
-  ClassDef(THcHallCSpectrometer,0) //A Hall A High Resolution Spectrometer
+  ClassDef(THcHallCSpectrometer,0) //A Hall C Spectrometer
 };
 
 #endif
diff --git a/src/THcHitList.cxx b/src/THcHitList.cxx
index 4659785a0495a78dc04e5fe89c67c1d5653d0700..c133fbfbcbdd65ec5b6da0cb960460125c33af1c 100644
--- a/src/THcHitList.cxx
+++ b/src/THcHitList.cxx
@@ -4,9 +4,9 @@
 //
 // THcHitList
 //
-// Add hitlist to the Hall A detector base
-// May not need to inherit from THaDetectorBase since we may end up
-// replacing most of the methods
+// Class to build a Hall C ENGINE style list of raw hits from the raw data.
+// Detectors that use hit lists need to inherit from this class
+// as well as THaTrackingDetector or THaNonTrackingDetector
 //
 //////////////////////////////////////////////////////////////////////////
 
@@ -30,7 +30,8 @@ THcHitList::~THcHitList() {
 
 void THcHitList::InitHitList(THaDetMap* detmap,
 				  const char *hitclass, Int_t maxhits) {
-  // Probably called by ReadDatabase
+  // Save the electronics to detector mapping
+  // Initialize a hit array of hits of class hitclass
 
   fRawHitList = new TClonesArray(hitclass, maxhits);
   fRawHitClass = fRawHitList->GetClass();
@@ -44,6 +45,14 @@ void THcHitList::InitHitList(THaDetMap* detmap,
 }
 
 Int_t THcHitList::DecodeToHitList( const THaEvData& evdata ) {
+  // Clear the hit list
+  // Find all populated channels belonging to the detector and add
+  // the data to the hitlist.  A given counter in the detector can have
+  // at most one entry in the hit list.  However, the raw "hit" can contain
+  // multiple signal types (e.g. ADC+, ADC-, TDC+, TDC-), or multiple
+  // hits for multihit tdcs.
+  // The hit list is sorted (by plane, counter) after filling.
+
   THcRawHit* rawhit;
   // cout << " Clearing TClonesArray " << endl;
   fRawHitList->Clear( );
diff --git a/src/THcHitList.h b/src/THcHitList.h
index 494866bcb875b326dc40d246e126a7dbc25c3383..040d4c061a70c19ef2106e06c34eaf35d1842f47 100644
--- a/src/THcHitList.h
+++ b/src/THcHitList.h
@@ -41,6 +41,6 @@ public:
 
 protected:
 
-  ClassDef(THcHitList,0)
+  ClassDef(THcHitList,0);  // List of raw hits sorted by plane, counter
 };
 #endif
diff --git a/src/THcHodoscope.cxx b/src/THcHodoscope.cxx
index a2c401064566f04d9b2771af18d799d2f856e1c0..202b97c3944f7c6b3c6e79efbc32c99f43c877bb 100644
--- a/src/THcHodoscope.cxx
+++ b/src/THcHodoscope.cxx
@@ -142,7 +142,7 @@ THaAnalysisObject::EStatus THcHodoscope::Init( const TDatime& date )
   // But it needs to happen before the sub detectors are initialized
   // so that they can get the pointer to the hitlist.
 
-  THcHitList::InitHitList(fDetMap, "THcHodoscopeHit", 100);
+  InitHitList(fDetMap, "THcHodoscopeHit", 100);
 
   EStatus status;
   // This triggers call of ReadDatabase and DefineVariables
@@ -596,7 +596,7 @@ Int_t THcHodoscope::Decode( const THaEvData& evdata )
 {
 
   // Get the Hall C style hitlist (fRawHitList) for this event
-  Int_t nhits = THcHitList::DecodeToHitList(evdata);
+  Int_t nhits = DecodeToHitList(evdata);
 
   if(gHaCuts->Result("Pedestal_event")) {
     Int_t nexthit = 0;
diff --git a/src/THcHodoscope.h b/src/THcHodoscope.h
index 7d18bc8d808b8ea6cead145c8c615e79544b0504..2c90d460172b2d0f00090210ff900c64502c9fe5 100644
--- a/src/THcHodoscope.h
+++ b/src/THcHodoscope.h
@@ -131,7 +131,7 @@ protected:
 
   void Setup(const char* name, const char* description);
 
-  ClassDef(THcHodoscope,0)   // Generic hodoscope class
+  ClassDef(THcHodoscope,0)   // Hodoscope detector
 };
 
 ////////////////////////////////////////////////////////////////////////////////
diff --git a/src/THcHodoscopeHit.h b/src/THcHodoscopeHit.h
index 0bac2d1a1f9a231325dfb83a2a31e58f1ef95e67..ef88875d11635a8a696bc1ac4ffdfb6a2439e0b1 100644
--- a/src/THcHodoscopeHit.h
+++ b/src/THcHodoscopeHit.h
@@ -6,8 +6,9 @@
 class THcHodoscopeHit : public THcRawHit {
 
  public:
+  friend class THcScintillatorPlane;
 
- THcHodoscopeHit(Int_t plane=0, Int_t counter=0) : THcRawHit(plane, counter), 
+  THcHodoscopeHit(Int_t plane=0, Int_t counter=0) : THcRawHit(plane, counter), 
     fADC_pos(-1), fADC_neg(-1),
     fTDC_pos(-1), fTDC_neg(-1) {
   }
@@ -23,16 +24,15 @@ class THcHodoscopeHit : public THcRawHit {
   //  virtual Bool_t  IsSortable () const {return kTRUE; }
   //  virtual Int_t   Compare(const TObject* obj) const;
 
+ protected:
   Int_t fADC_pos;
   Int_t fADC_neg;
   Int_t fTDC_pos;
   Int_t fTDC_neg;
 
- protected:
-
  private:
 
-  ClassDef(THcHodoscopeHit, 0);	// Hodoscope hit class
+  ClassDef(THcHodoscopeHit, 0);	// Raw Hodoscope hit
 };  
 
 #endif
diff --git a/src/THcParmList.cxx b/src/THcParmList.cxx
index d75c690c11fa07a916eed61a8f1867af33b24579..a645b9328ccfc58f65b410704299da7c003e122a 100644
--- a/src/THcParmList.cxx
+++ b/src/THcParmList.cxx
@@ -42,6 +42,17 @@ inline static bool IsComment( const string& s, string::size_type pos )
 
 void THcParmList::Load( const char* fname, Int_t RunNumber )
 {
+  // Read a CTP style parameter file.
+  //
+  // Parameter values and arrays of values are cached in a THaVarList
+  // and are available for use elsewhere in the analyzer.
+  // Text strings are saved in a THaTextvars list.
+  // Parameter files can contain "include" statements of the form
+  //   #include "filename"
+  //
+  // If a run number is given, ignore input until a line with a matching
+  // run number or run number range is found.  All parameters following
+  // the are read until a non matching run number or range is encountered.
 
   static const char* const whtspc = " \t";
 
@@ -420,6 +431,8 @@ Int_t THcParmList::LoadParmValues(const DBRequest* list, const char* prefix)
   // must be given, and the memory already allocated
   // NOTE: initial code taken wholesale from THaDBFile. 
   // GN 2012
+  // If prefix is specified, prepend each requested parameter name with
+  // the prefix.
   
   const DBRequest *ti = list;
   Int_t cnt=0;
@@ -561,6 +574,8 @@ Int_t THcParmList::ReadArray(const char* attrC, T* array, Int_t size)
 //_____________________________________________________________________________
 void THcParmList::PrintFull( Option_t* option ) const
 {
+  // Print all the numeric parameter desciptions and values.
+  // Print all the text parameters
   THaVarList::PrintFull(option);
   TextList->Print();
 }
diff --git a/src/THcRawDCHit.h b/src/THcRawDCHit.h
index 4eb2c55ad9755ce6a179807c415e38bd8dbe408f..5e077878e66b710a68183ce8618a465d0ba98ffb 100644
--- a/src/THcRawDCHit.h
+++ b/src/THcRawDCHit.h
@@ -8,6 +8,8 @@
 class THcRawDCHit : public THcRawHit {
 
 public:
+  friend class THcDriftChamberPlane;
+  friend class THcDC;
 
   THcRawDCHit(Int_t plane=0, Int_t counter=0) : THcRawHit(plane, counter), 
     fNHits(0) {
@@ -24,14 +26,14 @@ public:
   virtual Bool_t  IsSortable () const {return kTRUE; }
   virtual Int_t   Compare(const TObject* obj) const;
 
-  Int_t fNHits;
-  Int_t fTDC[MAXHITS];
 
 protected:
+  Int_t fNHits;
+  Int_t fTDC[MAXHITS];
 
 private:
 
-  ClassDef(THcRawDCHit, 0);	// DC hit class
+  ClassDef(THcRawDCHit, 0);	// Raw Drift Chamber hit
 };  
 
 #endif
diff --git a/src/THcRawHit.cxx b/src/THcRawHit.cxx
index 3e37972a189932d7dd987a50bcbdf8ec59388f37..e2cd54e6116145954a70011f6c9888519cec4dd6 100644
--- a/src/THcRawHit.cxx
+++ b/src/THcRawHit.cxx
@@ -10,12 +10,10 @@
 
 #include "THcRawHit.h"
 
-//THcRawHit::~THcRawHit()
-//{}
 
 Int_t THcRawHit::Compare(const TObject* obj) const
 {
-  // Compare to sort by plane and counter
+  // Comparision function for Sort().
 
   const THcRawHit* hit = dynamic_cast<const THcRawHit*>(obj);
 
diff --git a/src/THcRawHit.h b/src/THcRawHit.h
index 7372463c724a5e66229e48ad9bfb3b3bf270a6af..1ee7d16431cc7d2d6e95b32e2750e5ccdabdf3f4 100644
--- a/src/THcRawHit.h
+++ b/src/THcRawHit.h
@@ -39,7 +39,7 @@ public:
 
  private:
 
-  ClassDef(THcRawHit,0)      // Track ID abstract base class
+  ClassDef(THcRawHit,0)      // Raw Hit Base Class
 };
 
 #endif
diff --git a/src/THcRawShowerHit.h b/src/THcRawShowerHit.h
index 1671ddcbfcc7645315c2e99e7440c1b40927d067..76f0d140a5cae64d1dbff7ce837d276ee6da002f 100644
--- a/src/THcRawShowerHit.h
+++ b/src/THcRawShowerHit.h
@@ -6,8 +6,9 @@
 class THcRawShowerHit : public THcRawHit {
 
  public:
+  friend class THcShowerPlane;
 
- THcRawShowerHit(Int_t plane=0, Int_t counter=0) : THcRawHit(plane, counter), 
+  THcRawShowerHit(Int_t plane=0, Int_t counter=0) : THcRawHit(plane, counter), 
     fADC_pos(-1), fADC_neg(-1){
   }
   THcRawShowerHit& operator=( const THcRawShowerHit& );
@@ -22,14 +23,13 @@ class THcRawShowerHit : public THcRawHit {
   //  virtual Bool_t  IsSortable () const {return kTRUE; }
   //  virtual Int_t   Compare(const TObject* obj) const;
 
+ protected:
   Int_t fADC_pos;
   Int_t fADC_neg;
 
- protected:
-
  private:
 
-  ClassDef(THcRawShowerHit, 0);	// Shower hit class
+  ClassDef(THcRawShowerHit, 0);	// Raw Shower counter hit
 };  
 
 #endif
diff --git a/src/THcScintillatorPlane.h b/src/THcScintillatorPlane.h
index cb832fa7dd0975bf1eb0d064e6e6cb91a2e60cfb..9b5f33e5cc5a40300b3c93bfc7e7755d2ccb1bc1 100644
--- a/src/THcScintillatorPlane.h
+++ b/src/THcScintillatorPlane.h
@@ -113,7 +113,7 @@ class THcScintillatorPlane : public THaSubDetector {
   virtual Int_t  DefineVariables( EMode mode = kDefine );
   virtual void  InitializePedestals( );
 
-  ClassDef(THcScintillatorPlane,0)
+  ClassDef(THcScintillatorPlane,0); // Scintillator bars in a plane
 };
 #endif
 
diff --git a/src/THcShower.cxx b/src/THcShower.cxx
index 67c2ca0ef61d301fdb93e5c0542957b4b7dcdc5a..2047500b70ba5a58635c99363448b27371a4cf89 100644
--- a/src/THcShower.cxx
+++ b/src/THcShower.cxx
@@ -111,7 +111,7 @@ THaAnalysisObject::EStatus THcShower::Init( const TDatime& date )
   // Should probably put this in ReadDatabase as we will know the
   // maximum number of hits after setting up the detector map
 
-  THcHitList::InitHitList(fDetMap, "THcRawShowerHit", 100);
+  InitHitList(fDetMap, "THcRawShowerHit", 100);
 
   EStatus status;
   if( (status = THaNonTrackingDetector::Init( date )) )
@@ -514,7 +514,7 @@ Int_t THcShower::Decode( const THaEvData& evdata )
   Clear();
 
   // Get the Hall C style hitlist (fRawHitList) for this event
-  Int_t nhits = THcHitList::DecodeToHitList(evdata);
+  Int_t nhits = DecodeToHitList(evdata);
 
   if(gHaCuts->Result("Pedestal_event")) {
     Int_t nexthit = 0;
diff --git a/src/THcShower.h b/src/THcShower.h
index 4286a8252b1b169efb2b52fd473c49adf22a7b44..89e6c053558b36af11955fd09c1ed7f41838f587 100644
--- a/src/THcShower.h
+++ b/src/THcShower.h
@@ -197,7 +197,7 @@ protected:
 
   friend class THcShowerPlane;   //to access debug flags.
 
-  ClassDef(THcShower,0)          // Generic class
+  ClassDef(THcShower,0)          // Shower counter detector
 };
 
 ///////////////////////////////////////////////////////////////////////////////
diff --git a/src/THcShowerPlane.h b/src/THcShowerPlane.h
index 8cb7e141d6c2cf355d56a25a50f62dc98a3f1356..41fecdfcb29768015bca2e7ec96828da94a01e8b 100644
--- a/src/THcShowerPlane.h
+++ b/src/THcShowerPlane.h
@@ -147,6 +147,6 @@ protected:
   virtual Int_t  ReadDatabase( const TDatime& date );
   virtual Int_t  DefineVariables( EMode mode = kDefine );
   virtual void  InitializePedestals( );
-  ClassDef(THcShowerPlane,0)
+  ClassDef(THcShowerPlane,0); // Calorimeter bars in a plane
 };
 #endif
diff --git a/src/THcSignalHit.h b/src/THcSignalHit.h
index 6af80a6e68a203261d306336022d015a237a71cf..808c730b287d256ade1d35f8dab854c9c0445d7f 100644
--- a/src/THcSignalHit.h
+++ b/src/THcSignalHit.h
@@ -29,7 +29,7 @@ class THcSignalHit : public TObject {
   Int_t fPaddleNumber;
   Double_t fData;
 
-  ClassDef(THcSignalHit,0)
+  ClassDef(THcSignalHit,0); // Single signal value and wire/counter number
 };
 /////////////////////////////////////////////////////////////////
 #endif
diff --git a/src/THcSpacePoint.h b/src/THcSpacePoint.h
index bf63699e881b5d921b4aefea52ec1d3d7518d4c1..36faa3d347b911c4728e5baab1422ba3459b9b92 100644
--- a/src/THcSpacePoint.h
+++ b/src/THcSpacePoint.h
@@ -84,7 +84,7 @@ protected:
   Double_t fStub[4];
   // Should we also have a pointer back to the chamber object
 
-  ClassDef(THcSpacePoint,0)   // Drift Chamber class
+  ClassDef(THcSpacePoint,0);   // Space Point/stub track in a single drift chamber
 };
 
 ////////////////////////////////////////////////////////////////////////////////