diff --git a/ChangeLog b/ChangeLog
index 3816fc8f63..fc1e4aef7a 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,8 @@
+2005-05-20    <lgb@tandberg.net>
+
+	* configure.ac: Use AM_* flags for CLAGS,CXXFLAGS where we require
+	the values to be properly set.
+
 2005-05-03  Angus Leeming  <leeming@lyx.org>
 
 	* configure.ac: test for io.h and process.h.
diff --git a/boost/libs/filesystem/src/Makefile.am b/boost/libs/filesystem/src/Makefile.am
index 438d0edf8d..6765ad56d5 100644
--- a/boost/libs/filesystem/src/Makefile.am
+++ b/boost/libs/filesystem/src/Makefile.am
@@ -2,7 +2,7 @@ include $(top_srcdir)/config/common.am
 
 noinst_LTLIBRARIES = libboost_filesystem.la
 
-AM_CPPFLAGS = \
+AM_CPPFLAGS += \
 	$(PCH_FLAGS) \
 	-DBOOST_USER_CONFIG="<config.h>" \
 	$(BOOST_INCLUDES)
diff --git a/boost/libs/regex/src/Makefile.am b/boost/libs/regex/src/Makefile.am
index 7674459d66..21241e9e73 100644
--- a/boost/libs/regex/src/Makefile.am
+++ b/boost/libs/regex/src/Makefile.am
@@ -2,7 +2,7 @@ include $(top_srcdir)/config/common.am
 
 noinst_LTLIBRARIES = libboost_regex.la
 
-AM_CPPFLAGS = \
+AM_CPPFLAGS += \
 	$(PCH_FLAGS) \
 	-DBOOST_USER_CONFIG="<config.h>" \
 	$(BOOST_INCLUDES)
diff --git a/boost/libs/signals/src/Makefile.am b/boost/libs/signals/src/Makefile.am
index c84da747a5..99cee23980 100644
--- a/boost/libs/signals/src/Makefile.am
+++ b/boost/libs/signals/src/Makefile.am
@@ -2,7 +2,7 @@ include $(top_srcdir)/config/common.am
 
 noinst_LTLIBRARIES = libboost_signals.la
 
-AM_CPPFLAGS = \
+AM_CPPFLAGS += \
 	$(PCH_FLAGS) \
 	-DBOOST_USER_CONFIG="<config.h>" \
 	$(BOOST_INCLUDES)
diff --git a/config/lyxinclude.m4 b/config/lyxinclude.m4
index 15f28fe870..a1681c71e4 100644
--- a/config/lyxinclude.m4
+++ b/config/lyxinclude.m4
@@ -169,7 +169,7 @@ AC_ARG_ENABLE(warnings,
 	enable_warnings=no;
     fi;])
 if test x$enable_warnings = xyes ; then
-  lyx_flags="$lyx_flags warnings"
+  lyx_flags="warnings $lyx_flags"
   AC_DEFINE(WITH_WARNINGS, 1,
   [Define this if you want to see the warning directives put here and
    there by the developpers to get attention])
@@ -224,26 +224,39 @@ if test x$GXX = xyes; then
   if test "$ac_test_CXXFLAGS" = set; then
     CXXFLAGS="$ac_save_CXXFLAGS"
   else
-    case $gxx_version in
-      2.95.1)  CXXFLAGS="$lyx_opt -fpermissive -ftemplate-depth-30";;
-      2.95.*)  CXXFLAGS="$lyx_opt -Wno-non-template-friend -ftemplate-depth-30";;
-      2.96*)  CXXFLAGS="$lyx_opt -fno-exceptions -ftemplate-depth-30 -Wno-non-template-friend";;
-      3.1*)    CXXFLAGS="$lyx_opt -finline-limit=500 -fno-exceptions";;
-      3.2*|3.3*)    CXXFLAGS="$lyx_opt -fno-exceptions";;
-      3.4*|4.0*)
-	    CXXFLAGS="$lyx_opt -fno-exceptions"
-	    test $enable_pch = yes && lyx_pch_comp=yes
-	    ;;
-      *)       CXXFLAGS="$lyx_opt";;
-    esac
+      CFLAGS="$lyx_opt"
+      CXXFLAGS="$lyx_opt"
     if test x$enable_debug = xyes ; then
+        CFLAGS="-g $CFLAGS"
 	CXXFLAGS="-g $CXXFLAGS"
     fi
+    if test x$enable_warnings = xyes ; then
+        case $gxx_version in
+            2.*|3.1*|3.2*|3.3*)
+                CPPFLAGS="-W -Wall $CPPFLAGS"
+                ;;
+            *)
+                CPPFLAGS="-Wextra -Wall $CPPFLAGS "
+                ;;
+        esac
+    fi
   fi
+  case $gxx_version in
+      2.95.1)  AM_CXXFLAGS="-fpermissive -ftemplate-depth-30";;
+      2.95.*)  AM_CXXFLAGS="-Wno-non-template-friend -ftemplate-depth-30";;
+      2.96*)  AM_CXXFLAGS="-fno-exceptions -ftemplate-depth-30 -Wno-non-template-friend";;
+      3.1*)    AM_CXXFLAGS="-finline-limit=500 -fno-exceptions";;
+      3.2*|3.3*)    AM_CXXFLAGS="-fno-exceptions";;
+      3.4*|4.0*)
+          AM_CXXFLAGS="-fno-exceptions"
+          test $enable_pch = yes && lyx_pch_comp=yes
+          ;;
+      *)       AM_CXXFLAGS="";;
+  esac
   if test x$enable_stdlib_debug = xyes ; then
     case $gxx_version in
       3.4*|4.0*)
-        lyx_flags="$lyx_flags stdlib-debug"
+        lyx_flags="stdlib-debug $lyx_flags"
 	AC_DEFINE(_GLIBCXX_DEBUG, 1, [libstdc++ debug mode])
 	AC_DEFINE(_GLIBCXX_DEBUG_PEDANTIC, 1, [libstdc++ pedantic debug mode])
         ;;
@@ -252,27 +265,17 @@ if test x$GXX = xyes; then
   if test x$enable_concept_checks = xyes ; then
     case $gxx_version in
       3.3*)
-        lyx_flags="$lyx_flags concept-checks"
+        lyx_flags="concept-checks $lyx_flags"
         AC_DEFINE(_GLIBCPP_CONCEPT_CHECKS, 1, [libstdc++ concept checking])
 	;;
       3.4*|4.0*)
-        lyx_flags="$lyx_flags concept-checks"
+        lyx_flags="concept-checks $lyx_flags"
 	AC_DEFINE(_GLIBCXX_CONCEPT_CHECKS, 1, [libstdc++ concept checking])
 	;;
     esac
   fi
-  if test x$enable_warnings = xyes ; then
-    case $gxx_version in
-      2.*|3.1*|3.2*|3.3*)
-        CPPFLAGS="$CPPFLAGS -W -Wall"
-        ;;
-      *)
-        CPPFLAGS="$CPPFLAGS -Wextra -Wall"
-        ;;
-    esac
-  fi
 fi
-test "$lyx_pch_comp" = yes && lyx_flags="$lyx_flags pch"
+test "$lyx_pch_comp" = yes && lyx_flags="pch $lyx_flags"
 AM_CONDITIONAL(LYX_BUILD_PCH, test "$lyx_pch_comp" = yes)
 ])dnl
 
diff --git a/configure.ac b/configure.ac
index 22f641f306..9c953b608f 100644
--- a/configure.ac
+++ b/configure.ac
@@ -78,7 +78,7 @@ AC_ARG_ENABLE(assertions,
 	enable_assertions=no;
     fi;])
 if test "x$enable_assertions" = xyes ; then
-   lyx_flags="$lyx_flags assertions"
+   lyx_flags="assertions $lyx_flags"
    AC_DEFINE(ENABLE_ASSERTIONS,1,
     [Define if you want assertions to be enabled in the code])
 fi
@@ -112,7 +112,7 @@ if test x$lyx_use_aiksaurus != xno; then
 AC_CHECK_LIB(Aiksaurus, main,
 	[AC_DEFINE(HAVE_LIBAIKSAURUS,1,[Define this if you have the AikSaurus library])
 	 AIKSAURUS_LIBS="-lAiksaurus"
-	 lyx_flags="$lyx_flags aiksaurus"
+	 lyx_flags="aiksaurus $lyx_flags"
 	])
 AC_CHECK_HEADER(Aiksaurus.h,[
   ac_cv_header_aiksaurus_h=yes
@@ -269,7 +269,7 @@ if test $use_compression=true ; then
 	AC_CHECK_LIB(z, gzopen,[use_compression=true;LIBS="$LIBS -lz"], use_compression=false)
 	if test $use_compression = true ; then
 		AC_DEFINE(USE_COMPRESSION, 1, [Define as 1 if you want to support compressed files.])
-		lyx_flags="$lyx_flags compression"
+		lyx_flags="compression $lyx_flags"
 	fi
 fi
 AM_CONDITIONAL(USE_COMPRESSION, test x$use_compression = xtrue)
@@ -301,12 +301,15 @@ real_bindir=`eval "echo \`eval \"echo ${bindir}\"\`"`
 real_datadir=`eval "echo \`eval \"echo ${datadir}/${PACKAGE}\"\`"`
 VERSION_INFO="Configuration\n\
   Host type:                      ${host}\n\
-  Special build flags:           ${lyx_flags}\n\
-  C   Compiler:                   ${CC}\n\
+  Special build flags:            ${lyx_flags}\n\
+  C   Compiler:                   ${CC} ${CC_VERSION}\n\
+  C   Compiler LyX flags:         ${AM_CPPFLAGS} ${AM_CFLAGS}\n\
   C   Compiler flags:             ${CPPFLAGS} ${CFLAGS}\n\
   C++ Compiler:                   ${CXX} ${CXX_VERSION}\n\
+  C++ Compiler LyX flags:         ${AM_CPPFLAGS} ${AM_CXXFLAGS}\n\
   C++ Compiler flags:             ${CPPFLAGS} ${CXXFLAGS}\n\
-  Linker flags:                   ${LDFLAGS}\n\
+  Linker flags:                   ${AM_LDFLAGS}\n\
+  Linker user flags:              ${LDFLAGS}\n\
 ${FRONTEND_INFO}\
   Packaging:                      ${lyx_use_packaging}\n\
   LyX binary dir:                 ${real_bindir}\n\
@@ -315,6 +318,10 @@ ${FRONTEND_INFO}\
 
 AC_SUBST(VERSION_INFO)
 AC_SUBST(RPM_FRONTEND)
+AC_SUBST(AM_CPPFLAGS)
+AC_SUBST(AM_CXXFLAGS)
+AC_SUBST(AM_CFLAGS)
+AC_SUBST(AM_LDFLAGS)
 
 ## Some config.h stuff
 
diff --git a/src/Makefile.am b/src/Makefile.am
index 6b556d44d1..ef9f546742 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -53,7 +53,7 @@ lyx$(EXEEXT): $(FRONTENDS_PROGS)
 
 BUILT_SOURCES = version.C
 
-AM_CPPFLAGS = $(PCH_FLAGS) $(BOOST_INCLUDES)
+AM_CPPFLAGS += $(PCH_FLAGS) $(BOOST_INCLUDES)
 
 if USE_ASPELL
 ASPELL = aspell.C aspell_local.h
diff --git a/src/client/Makefile.am b/src/client/Makefile.am
index 9454d542d9..feb68401fb 100644
--- a/src/client/Makefile.am
+++ b/src/client/Makefile.am
@@ -8,7 +8,7 @@ man_MANS = lyxclient.1
 
 bin_PROGRAMS = lyxclient
 
-AM_CPPFLAGS = $(PCH_FLAGS) -I$(srcdir)/.. $(BOOST_INCLUDES)
+AM_CPPFLAGS += $(PCH_FLAGS) -I$(srcdir)/.. $(BOOST_INCLUDES)
 
 BOOST_LIBS = $(BOOST_REGEX) $(BOOST_FILESYSTEM)
 
diff --git a/src/frontends/Makefile.am b/src/frontends/Makefile.am
index 14a6613d3f..a310e8cc8c 100644
--- a/src/frontends/Makefile.am
+++ b/src/frontends/Makefile.am
@@ -6,7 +6,7 @@ DIST_SUBDIRS = controllers xforms qt2 gtk
 
 noinst_LTLIBRARIES = libfrontends.la
 
-AM_CPPFLAGS = $(PCH_FLAGS) -I$(srcdir)/..  $(BOOST_INCLUDES)
+AM_CPPFLAGS += $(PCH_FLAGS) -I$(srcdir)/..  $(BOOST_INCLUDES)
 
 libfrontends_la_SOURCES = \
 	Alert.C \
diff --git a/src/frontends/controllers/Makefile.am b/src/frontends/controllers/Makefile.am
index 17d23becfe..618777ac1b 100644
--- a/src/frontends/controllers/Makefile.am
+++ b/src/frontends/controllers/Makefile.am
@@ -4,7 +4,7 @@ EXTRA_DIST = BCView.tmpl
 
 noinst_LTLIBRARIES = libcontrollers.la
 
-AM_CPPFLAGS = $(PCH_FLAGS) -I$(top_srcdir)/src $(BOOST_INCLUDES)
+AM_CPPFLAGS += $(PCH_FLAGS) -I$(top_srcdir)/src $(BOOST_INCLUDES)
 
 libcontrollers_la_SOURCES= \
 	Dialog.C \
diff --git a/src/frontends/gtk/Makefile.am b/src/frontends/gtk/Makefile.am
index ba192dacbc..e8235cb84e 100644
--- a/src/frontends/gtk/Makefile.am
+++ b/src/frontends/gtk/Makefile.am
@@ -4,7 +4,7 @@ SUBDIRS = gimages glade
 
 noinst_LTLIBRARIES = libgtk.la
 
-AM_CPPFLAGS = \
+AM_CPPFLAGS += \
 	$(PCH_FLAGS) \
 	-I$(top_srcdir)/images \
 	-I$(top_srcdir)/src \
diff --git a/src/frontends/qt2/Makefile.am b/src/frontends/qt2/Makefile.am
index 36298be8ca..afaf382cef 100644
--- a/src/frontends/qt2/Makefile.am
+++ b/src/frontends/qt2/Makefile.am
@@ -10,7 +10,7 @@ noinst_LTLIBRARIES = libqt2.la
 libqt2_la_LDFLAGS = $(QT_LDFLAGS)
 libqt2_la_LIBADD = $(QT_LIB) ui/*.lo moc/*.lo ui/moc/*.lo
 
-AM_CPPFLAGS = \
+AM_CPPFLAGS += \
 	$(QT_CPPFLAGS) \
 	$(PCH_FLAGS) \
 	-I$(top_srcdir)/src \
diff --git a/src/frontends/qt2/moc/Makefile.am b/src/frontends/qt2/moc/Makefile.am
index 555814197b..bb3afe28aa 100644
--- a/src/frontends/qt2/moc/Makefile.am
+++ b/src/frontends/qt2/moc/Makefile.am
@@ -3,7 +3,7 @@ include $(srcdir)/../Makefile.dialogs
 
 DISTCLEANFILES += *.C
 
-AM_CPPFLAGS = \
+AM_CPPFLAGS += \
 	$(QT_CPPFLAGS) -DQT_NO_TRANSLATION \
 	$(PCH_FLAGS) \
 	-I$(top_srcdir)/src \
diff --git a/src/frontends/qt2/ui/Makefile.am b/src/frontends/qt2/ui/Makefile.am
index c08a386edb..de7f55e6c8 100644
--- a/src/frontends/qt2/ui/Makefile.am
+++ b/src/frontends/qt2/ui/Makefile.am
@@ -7,7 +7,7 @@ SUBDIRS = . moc
 
 EXTRA_DIST = QPreambleDialogBase.ui $(UIFILES)
 
-AM_CPPFLAGS = \
+AM_CPPFLAGS += \
 	$(QT_CPPFLAGS) -DQT_NO_TRANSLATION \
 	$(PCH_FLAGS) \
 	-I$(top_srcdir)/src \
diff --git a/src/frontends/qt2/ui/moc/Makefile.am b/src/frontends/qt2/ui/moc/Makefile.am
index 1cac7d84bf..0540aeb178 100644
--- a/src/frontends/qt2/ui/moc/Makefile.am
+++ b/src/frontends/qt2/ui/moc/Makefile.am
@@ -3,7 +3,7 @@ include $(srcdir)/../../Makefile.dialogs
 
 DISTCLEANFILES += $(UIFILES:.ui=_moc.C)
 
-AM_CPPFLAGS = \
+AM_CPPFLAGS += \
 	$(QT_CPPFLAGS) -DQT_NO_TRANSLATION \
 	$(PCH_FLAGS) \
 	-I$(top_srcdir)/src \
diff --git a/src/frontends/xforms/Makefile.am b/src/frontends/xforms/Makefile.am
index e8d4378cc4..e8155c8fa1 100644
--- a/src/frontends/xforms/Makefile.am
+++ b/src/frontends/xforms/Makefile.am
@@ -7,7 +7,7 @@ BUILT_SOURCES = lyx_forms.h lyx_xpm.h
 
 EXTRA_DIST = lyx_forms.h.in lyx_xpm.h.in
 
-AM_CPPFLAGS = \
+AM_CPPFLAGS += \
 	-I$(top_srcdir)/images \
 	-I$(top_srcdir)/src \
 	-I$(top_srcdir)/src/frontends \
@@ -16,7 +16,7 @@ AM_CPPFLAGS = \
 
 # This cannot be put in AM_CPPFLAGS since that is used both for C and C++
 # And the precompiled header is setup only for C++
-AM_CXXFLAGS = $(PCH_FLAGS)
+AM_CXXFLAGS += $(PCH_FLAGS)
 
 noinst_LTLIBRARIES = libxforms.la
 
diff --git a/src/frontends/xforms/forms/Makefile.am b/src/frontends/xforms/forms/Makefile.am
index 0e66f04a61..66d42463f2 100644
--- a/src/frontends/xforms/forms/Makefile.am
+++ b/src/frontends/xforms/forms/Makefile.am
@@ -5,7 +5,7 @@ DISTCLEANFILES += $(SRCS:.fd=.C) $(SRCS:.fd=.h) $(SRCS:.fd=.c)
 EXTRA_DIST = fdfixc.sed fdfixh.sed fdfix.sh tmp_str.sed README $(SRCS)
 
 # For (forms_fwd.h, forms_gettext.h) and support/std_string.h, respectively.
-AM_CPPFLAGS = $(PCH_FLAGS) -I$(srcdir)/..  -I$(top_srcdir)/src -I..
+AM_CPPFLAGS += $(PCH_FLAGS) -I$(srcdir)/..  -I$(top_srcdir)/src -I..
 
 noinst_LTLIBRARIES = libfdesign.la
 
diff --git a/src/graphics/Makefile.am b/src/graphics/Makefile.am
index 0891b93b3f..923fd53eb3 100644
--- a/src/graphics/Makefile.am
+++ b/src/graphics/Makefile.am
@@ -2,7 +2,7 @@ include $(top_srcdir)/config/common.am
 
 noinst_LTLIBRARIES = libgraphics.la
 
-AM_CPPFLAGS = $(PCH_FLAGS) -I$(srcdir)/.. $(BOOST_INCLUDES)
+AM_CPPFLAGS += $(PCH_FLAGS) -I$(srcdir)/.. $(BOOST_INCLUDES)
 
 libgraphics_la_SOURCES = \
 	GraphicsCache.h \
diff --git a/src/insets/Makefile.am b/src/insets/Makefile.am
index 80b87e08b4..da08b05051 100644
--- a/src/insets/Makefile.am
+++ b/src/insets/Makefile.am
@@ -6,7 +6,7 @@ EXTRA_DIST = \
 	insettheorem.C \
 	insettheorem.h
 
-AM_CPPFLAGS = $(PCH_FLAGS) -I$(srcdir)/.. $(BOOST_INCLUDES)
+AM_CPPFLAGS += $(PCH_FLAGS) -I$(srcdir)/.. $(BOOST_INCLUDES)
 
 libinsets_la_SOURCES = \
 	mailinset.C \
diff --git a/src/mathed/Makefile.am b/src/mathed/Makefile.am
index 7d5554c2ee..ae7aef24f5 100644
--- a/src/mathed/Makefile.am
+++ b/src/mathed/Makefile.am
@@ -4,7 +4,7 @@ EXTRA_DIST = formulamacro.C
 
 noinst_LTLIBRARIES = libmathed.la
 
-AM_CPPFLAGS = $(PCH_FLAGS) -I$(srcdir)/.. $(BOOST_INCLUDES)
+AM_CPPFLAGS += $(PCH_FLAGS) -I$(srcdir)/.. $(BOOST_INCLUDES)
 
 libmathed_la_SOURCES = \
 	textpainter.C \
diff --git a/src/support/Makefile.am b/src/support/Makefile.am
index 55095ed187..da402acf27 100644
--- a/src/support/Makefile.am
+++ b/src/support/Makefile.am
@@ -14,7 +14,7 @@ endif
 
 BUILT_SOURCES = package.C
 
-AM_CPPFLAGS = $(PCH_FLAGS) -I$(srcdir)/.. $(BOOST_INCLUDES)
+AM_CPPFLAGS += $(PCH_FLAGS) -I$(srcdir)/.. $(BOOST_INCLUDES)
 
 libsupport_la_SOURCES = \
 	FileMonitor.h \
diff --git a/src/support/tests/Makefile.am b/src/support/tests/Makefile.am
index 8f1c3c8c29..42700c411f 100644
--- a/src/support/tests/Makefile.am
+++ b/src/support/tests/Makefile.am
@@ -10,7 +10,7 @@ check_PROGRAMS = \
 	convert \
 	lstrings
 
-AM_CPPFLAGS = $(BOOST_INCLUDES)
+AM_CPPFLAGS += $(BOOST_INCLUDES)
 
 convert_LDADD = ../convert.o
 convert_SOURCES = \
diff --git a/src/tex2lyx/Makefile.am b/src/tex2lyx/Makefile.am
index c7bcab1d88..ce7c147619 100644
--- a/src/tex2lyx/Makefile.am
+++ b/src/tex2lyx/Makefile.am
@@ -13,7 +13,7 @@ DISTCLEANFILES += $(BUILT_SOURCES)
 
 bin_PROGRAMS = tex2lyx
 
-AM_CPPFLAGS = $(PCH_FLAGS) -I$(srcdir)/.. $(BOOST_INCLUDES)
+AM_CPPFLAGS += $(PCH_FLAGS) -I$(srcdir)/.. $(BOOST_INCLUDES)
 
 BOOST_LIBS = $(BOOST_REGEX) $(BOOST_FILESYSTEM)