--- trunk/configure	2006/09/04 13:37:15	1036
+++ trunk/configure	2006/10/23 18:11:06	1085
@@ -13603,7 +13603,7 @@ ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
 ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
 
     save_CXXFLAGS="$CXXFLAGS"
-    CXXFLAGS="$CXXFLAGS -I$CGAL_INCLDIR -I$CGAL_INCLCONFDIR"
+    CXXFLAGS="$CXXFLAGS $CGAL_CXXFLAGS -I$CGAL_INCLDIR -I$CGAL_INCLCONFDIR"
     if test "${ac_cv_header_CGAL_Cartesian_h+set}" = set; then
   echo "$as_me:$LINENO: checking for CGAL/Cartesian.h" >&5
 echo $ECHO_N "checking for CGAL/Cartesian.h... $ECHO_C" >&6
@@ -13800,7 +13800,7 @@ echo "${ECHO_T}no" >&6
 
       CGAL_LIBS="$CGAL_LIBS -lm"
 
-      CGAL_CXXFLAGS="-ftemplate-depth-50"
+      CGAL_CXXFLAGS="-ftemplate-depth-50 $CGAL_CXXFLAGS"
 
       echo "$as_me:$LINENO: result: CGAL_USES_LEDA=     $CGAL_USES_LEDA" >&5
 echo "${ECHO_T}CGAL_USES_LEDA=     $CGAL_USES_LEDA" >&6
@@ -13830,7 +13830,7 @@ save_CXXFLAGS_CHECK_CXX_LIB="$CXXFLAGS"
       echo "$as_me:$LINENO: checking for ::CGAL::Cartesian<int>::Point_2 in -lCGAL" >&5
 echo $ECHO_N "checking for ::CGAL::Cartesian<int>::Point_2 in -lCGAL... $ECHO_C" >&6
 save_CXXFLAGS_CHECK_CXX_LIB="$CXXFLAGS"
-CXXFLAGS="$CXXFLAGS -I$CGAL_INCLDIR -I$CGAL_INCLCONFDIR"
+CXXFLAGS="$CXXFLAGS $CGAL_CXXFLAGS -I$CGAL_INCLDIR -I$CGAL_INCLCONFDIR"
 save_LIBS_CHECK_CXX_LIB="$LIBS"
 LIBS="-lCGAL  $LIBS"
 cat >conftest.$ac_ext <<_ACEOF
@@ -14106,7 +14106,7 @@ fi
 
 
 
-                                                            ac_config_files="$ac_config_files make/Makefile src/utils/Makefile src/applications/nanoRodBuilder/Makefile src/applications/utilities/affineScale src/applications/utilities/waterBoxer scripts/filepp"
+                                        ac_config_files="$ac_config_files make/Makefile src/utils/Makefile src/applications/nanoRodBuilder/Makefile scripts/filepp"
 
 
 cat >confcache <<\_ACEOF
@@ -14640,8 +14640,6 @@ do
   "make/Makefile" ) CONFIG_FILES="$CONFIG_FILES make/Makefile" ;;
   "src/utils/Makefile" ) CONFIG_FILES="$CONFIG_FILES src/utils/Makefile" ;;
   "src/applications/nanoRodBuilder/Makefile" ) CONFIG_FILES="$CONFIG_FILES src/applications/nanoRodBuilder/Makefile" ;;
-  "src/applications/utilities/affineScale" ) CONFIG_FILES="$CONFIG_FILES src/applications/utilities/affineScale" ;;
-  "src/applications/utilities/waterBoxer" ) CONFIG_FILES="$CONFIG_FILES src/applications/utilities/waterBoxer" ;;
   "scripts/filepp" ) CONFIG_FILES="$CONFIG_FILES scripts/filepp" ;;
   "src/getopt.h" ) CONFIG_LINKS="$CONFIG_LINKS src/getopt.h:src/utils/gnugetopt.h" ;;
   "src/config.h" ) CONFIG_HEADERS="$CONFIG_HEADERS src/config.h" ;;
@@ -15054,8 +15052,6 @@ s,@INSTALL@,$ac_INSTALL,;t t
     make/Makefile ) chmod 0755 scripts/* ;;
     src/utils/Makefile ) chmod 0755 scripts/* ;;
     src/applications/nanoRodBuilder/Makefile ) chmod 0755 scripts/* ;;
-    src/applications/utilities/affineScale ) chmod 0755 scripts/* ;;
-    src/applications/utilities/waterBoxer ) chmod 0755 scripts/* ;;
     scripts/filepp ) chmod 0755 scripts/* ;;
   esac
 done