Modified Doxygen configuration to correctly produce API documentation

Doxyfile.in

@@ -84,7 +84,9 @@ EXCLUDE_SYMLINKS       = NO
 EXCLUDE_PATTERNS       = */tests/* \
                          */src/* \
                          */.svn/*
-EXCLUDE_SYMBOLS        = 
+EXCLUDE_SYMBOLS        = StandardMMForceField::*Info \
+                         GBSAOBCForceField::AtomInfo \
+                         System::ConstraintInfo
 EXAMPLE_PATH           = 
 EXAMPLE_PATTERNS       = 
 EXAMPLE_RECURSIVE      = NO
@@ -133,7 +135,7 @@ TREEVIEW_WIDTH         = 250
 #---------------------------------------------------------------------------
 # configuration options related to the LaTeX output
 #---------------------------------------------------------------------------
-GENERATE_LATEX         = YES
+GENERATE_LATEX         = NO
 LATEX_OUTPUT           = latex
 LATEX_CMD_NAME         = latex
 MAKEINDEX_CMD_NAME     = makeindex
@@ -187,15 +189,15 @@ ENABLE_PREPROCESSING   = YES
 MACRO_EXPANSION        = YES
 EXPAND_ONLY_PREDEF     = YES
 SEARCH_INCLUDES        = YES
-INCLUDE_PATH           = "@SimTK_SDK@/core/include"
+INCLUDE_PATH           = 
 INCLUDE_FILE_PATTERNS  = 
-PREDEFINED             = SimTK_SIMBODY_EXPORT=
-EXPAND_AS_DEFINED      = SimTK_PIMPL_DOWNCAST
+PREDEFINED             = 
+EXPAND_AS_DEFINED      = 
 SKIP_FUNCTION_MACROS   = YES
 #---------------------------------------------------------------------------
 # Configuration::additions related to external references   
 #---------------------------------------------------------------------------
-TAGFILES               = "@SimTK_SDK@/core/doc/api/SimTKsimmath/SimTKsimmathDoxygenTagFile"="../SimTKsimmath" "@SimTK_SDK@/core/doc/api/SimTKcommon/SimTKcommonDoxygenTagFile"="../SimTKcommon"
+TAGFILES               = 
 GENERATE_TAGFILE       = "html/@PROJECT_NAME@DoxygenTagfile"
 ALLEXTERNALS           = NO
 EXTERNAL_GROUPS        = YES
@@ -204,7 +206,7 @@ PERL_PATH              = /usr/bin/perl
 # Configuration options related to the dot tool   
 #---------------------------------------------------------------------------
 CLASS_DIAGRAMS         = YES
-MSCGEN_PATH            = /Developer/Applications/Doxygen.app/Contents/Resources/
+MSCGEN_PATH            = /Applications/Doxygen.app/Contents/Resources/
 HIDE_UNDOC_RELATIONS   = YES
 HAVE_DOT               = NO
 CLASS_GRAPH            = YES