diff --git a/ChangeLog b/ChangeLog
index 79184f2..eda7e88 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,13 @@
+2003-04-27  Adam Fedor  <fedor@gnu.org>
+
+	* Updates for filesystem change.
+	* GNUmakefile (GNUSTEP_MAKEFILES): Remove
+	* Documentation/GNUmakefile, Source/GNUmakefile,
+	Source/*/GNUmakefile, Tools/GNUmakefile: Idem
+	* configure.ac: Replace $GNUSTEP_SYSTEM_ROOT/Makefiles with
+	$GNUSTEP_MAKEFILES.  Replace Libraries with Library/Libraries.
+	Replace Headers with Library/Headers.
+
 2003-03-01  Fred Kiefer <FredKiefer@gmx.de>
 
 	* Source/winlib/Win32FontInfo.m
diff --git a/Documentation/GNUmakefile b/Documentation/GNUmakefile
index b9f93f6..733fc7a 100644
--- a/Documentation/GNUmakefile
+++ b/Documentation/GNUmakefile
@@ -23,8 +23,6 @@
 # Install into the system root by default
 GNUSTEP_INSTALLATION_DIR = $(GNUSTEP_SYSTEM_ROOT)
 
-GNUSTEP_MAKEFILES = $(GNUSTEP_SYSTEM_ROOT)/Makefiles
-
 GNUSTEP_LOCAL_ADDITIONAL_MAKEFILES=../back.make
 include $(GNUSTEP_MAKEFILES)/common.make
 
diff --git a/GNUmakefile b/GNUmakefile
index 01ecc0c..5fc51b4 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -30,8 +30,6 @@ PACKAGE_NEEDS_CONFIGURE = YES
 
 CVS_MODULE_NAME = back
 
-GNUSTEP_MAKEFILES = $(GNUSTEP_SYSTEM_ROOT)/Makefiles
-
 GNUSTEP_LOCAL_ADDITIONAL_MAKEFILES=back.make
 include $(GNUSTEP_MAKEFILES)/common.make
 
diff --git a/Source/GNUmakefile b/Source/GNUmakefile
index f096434..5b65c70 100644
--- a/Source/GNUmakefile
+++ b/Source/GNUmakefile
@@ -25,8 +25,6 @@
 # Install into the system root by default
 GNUSTEP_INSTALLATION_DIR = $(GNUSTEP_SYSTEM_ROOT)
 
-GNUSTEP_MAKEFILES = $(GNUSTEP_SYSTEM_ROOT)/Makefiles
-
 include $(GNUSTEP_MAKEFILES)/common.make
 
 include ../config.make
diff --git a/Source/art/GNUmakefile b/Source/art/GNUmakefile
index 9eec0f9..536a1a6 100644
--- a/Source/art/GNUmakefile
+++ b/Source/art/GNUmakefile
@@ -25,8 +25,6 @@
 
 GNUSTEP_INSTALLATION_DIR = $(GNUSTEP_SYSTEM_ROOT)
 
-GNUSTEP_MAKEFILES = $(GNUSTEP_SYSTEM_ROOT)/Makefiles
-
 GNUSTEP_LOCAL_ADDITIONAL_MAKEFILES=../../back.make
 include $(GNUSTEP_MAKEFILES)/common.make
 
diff --git a/Source/gsc/GNUmakefile b/Source/gsc/GNUmakefile
index b540c6b..2b1de6a 100644
--- a/Source/gsc/GNUmakefile
+++ b/Source/gsc/GNUmakefile
@@ -27,8 +27,6 @@
 
 GNUSTEP_INSTALLATION_DIR = $(GNUSTEP_SYSTEM_ROOT)
 
-GNUSTEP_MAKEFILES = $(GNUSTEP_SYSTEM_ROOT)/Makefiles
-
 GNUSTEP_LOCAL_ADDITIONAL_MAKEFILES=../../back.make
 include $(GNUSTEP_MAKEFILES)/common.make
 
diff --git a/Source/win32/GNUmakefile b/Source/win32/GNUmakefile
index 442ebf8..5cf8251 100644
--- a/Source/win32/GNUmakefile
+++ b/Source/win32/GNUmakefile
@@ -27,8 +27,6 @@
 
 GNUSTEP_INSTALLATION_DIR = $(GNUSTEP_SYSTEM_ROOT)
 
-GNUSTEP_MAKEFILES = $(GNUSTEP_SYSTEM_ROOT)/Makefiles
-
 GNUSTEP_LOCAL_ADDITIONAL_MAKEFILES=../../back.make
 
 include $(GNUSTEP_MAKEFILES)/common.make
diff --git a/Source/winlib/GNUmakefile b/Source/winlib/GNUmakefile
index 7840831..a038e25 100644
--- a/Source/winlib/GNUmakefile
+++ b/Source/winlib/GNUmakefile
@@ -24,8 +24,6 @@
 
 GNUSTEP_INSTALLATION_DIR = $(GNUSTEP_SYSTEM_ROOT)
 
-GNUSTEP_MAKEFILES = $(GNUSTEP_SYSTEM_ROOT)/Makefiles
-
 GNUSTEP_LOCAL_ADDITIONAL_MAKEFILES=../../back.make
 include $(GNUSTEP_MAKEFILES)/common.make
 
diff --git a/Source/x11/GNUmakefile b/Source/x11/GNUmakefile
index 1985fc2..51edf93 100644
--- a/Source/x11/GNUmakefile
+++ b/Source/x11/GNUmakefile
@@ -27,8 +27,6 @@
 
 GNUSTEP_INSTALLATION_DIR = $(GNUSTEP_SYSTEM_ROOT)
 
-GNUSTEP_MAKEFILES = $(GNUSTEP_SYSTEM_ROOT)/Makefiles
-
 GNUSTEP_LOCAL_ADDITIONAL_MAKEFILES=../../back.make
 
 include $(GNUSTEP_MAKEFILES)/common.make
diff --git a/Source/xdps/GNUmakefile b/Source/xdps/GNUmakefile
index 7c2bdaa..27bb7b3 100644
--- a/Source/xdps/GNUmakefile
+++ b/Source/xdps/GNUmakefile
@@ -27,8 +27,6 @@
 
 GNUSTEP_INSTALLATION_DIR = $(GNUSTEP_SYSTEM_ROOT)
 
-GNUSTEP_MAKEFILES = $(GNUSTEP_SYSTEM_ROOT)/Makefiles
-
 GNUSTEP_LOCAL_ADDITIONAL_MAKEFILES=../../back.make
 include $(GNUSTEP_MAKEFILES)/common.make
 
diff --git a/Source/xlib/GNUmakefile b/Source/xlib/GNUmakefile
index 913dbf8..d0f2ce5 100644
--- a/Source/xlib/GNUmakefile
+++ b/Source/xlib/GNUmakefile
@@ -27,8 +27,6 @@
 
 GNUSTEP_INSTALLATION_DIR = $(GNUSTEP_SYSTEM_ROOT)
 
-GNUSTEP_MAKEFILES = $(GNUSTEP_SYSTEM_ROOT)/Makefiles
-
 GNUSTEP_LOCAL_ADDITIONAL_MAKEFILES=../../back.make
 include $(GNUSTEP_MAKEFILES)/common.make
 
diff --git a/Tools/GNUmakefile b/Tools/GNUmakefile
index 7f82fed..e435d44 100644
--- a/Tools/GNUmakefile
+++ b/Tools/GNUmakefile
@@ -24,8 +24,6 @@
 
 GNUSTEP_INSTALLATION_DIR = $(GNUSTEP_SYSTEM_ROOT)
 
-GNUSTEP_MAKEFILES = $(GNUSTEP_SYSTEM_ROOT)/Makefiles
-
 GNUSTEP_LOCAL_ADDITIONAL_MAKEFILES=../back.make
 include $(GNUSTEP_MAKEFILES)/common.make
 
diff --git a/configure b/configure
index 2134a33..7cea215 100755
--- a/configure
+++ b/configure
@@ -897,7 +897,7 @@ esac
 # Don't blindly perform a `cd "$ac_dir"/$ac_foo && pwd` since $ac_foo can be
 # absolute.
 ac_abs_builddir=`cd "$ac_dir" && cd $ac_builddir && pwd`
-ac_abs_top_builddir=`cd "$ac_dir" && cd ${ac_top_builddir}. && pwd`
+ac_abs_top_builddir=`cd "$ac_dir" && cd $ac_top_builddir && pwd`
 ac_abs_srcdir=`cd "$ac_dir" && cd $ac_srcdir && pwd`
 ac_abs_top_srcdir=`cd "$ac_dir" && cd $ac_top_srcdir && pwd`
 
@@ -1220,7 +1220,7 @@ fi
 # Use config.guess, config.sub and install-sh provided by gnustep-make
 #--------------------------------------------------------------------
 ac_aux_dir=
-for ac_dir in $GNUSTEP_SYSTEM_ROOT/Makefiles $srcdir/$GNUSTEP_SYSTEM_ROOT/Makefiles; do
+for ac_dir in $GNUSTEP_MAKEFILES $srcdir/$GNUSTEP_MAKEFILES; do
   if test -f $ac_dir/install-sh; then
     ac_aux_dir=$ac_dir
     ac_install_sh="$ac_aux_dir/install-sh -c"
@@ -1236,8 +1236,8 @@ for ac_dir in $GNUSTEP_SYSTEM_ROOT/Makefiles $srcdir/$GNUSTEP_SYSTEM_ROOT/Makefi
   fi
 done
 if test -z "$ac_aux_dir"; then
-  { { echo "$as_me:$LINENO: error: cannot find install-sh or install.sh in $GNUSTEP_SYSTEM_ROOT/Makefiles $srcdir/$GNUSTEP_SYSTEM_ROOT/Makefiles" >&5
-echo "$as_me: error: cannot find install-sh or install.sh in $GNUSTEP_SYSTEM_ROOT/Makefiles $srcdir/$GNUSTEP_SYSTEM_ROOT/Makefiles" >&2;}
+  { { echo "$as_me:$LINENO: error: cannot find install-sh or install.sh in $GNUSTEP_MAKEFILES $srcdir/$GNUSTEP_MAKEFILES" >&5
+echo "$as_me: error: cannot find install-sh or install.sh in $GNUSTEP_MAKEFILES $srcdir/$GNUSTEP_MAKEFILES" >&2;}
    { (exit 1); exit 1; }; }
 fi
 ac_config_guess="$SHELL $ac_aux_dir/config.guess"
@@ -2037,8 +2037,6 @@ build_cpu=`echo $ac_cv_build | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\1/'`
 build_vendor=`echo $ac_cv_build | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\2/'`
 build_os=`echo $ac_cv_build | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\3/'`
 
-test -z "$build_alias" &&
-  build_alias=$ac_cv_build
 
 echo "$as_me:$LINENO: checking host system type" >&5
 echo $ECHO_N "checking host system type... $ECHO_C" >&6
@@ -2061,8 +2059,6 @@ host_cpu=`echo $ac_cv_host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\1/'`
 host_vendor=`echo $ac_cv_host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\2/'`
 host_os=`echo $ac_cv_host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\3/'`
 
-test -z "$host_alias" &&
-  host_alias=$ac_cv_host
 
 echo "$as_me:$LINENO: checking target system type" >&5
 echo $ECHO_N "checking target system type... $ECHO_C" >&6
@@ -2092,23 +2088,20 @@ test -n "$target_alias" &&
   test "$program_prefix$program_suffix$program_transform_name" = \
     NONENONEs,x,x, &&
   program_prefix=${target_alias}-
-test -z "$target_alias" &&
-  target_alias=$ac_cv_target
-
 
 #--------------------------------------------------------------------
 # The following is so that headers and custom libraries
 # in the GNUstep root are used before the standard ones
 #--------------------------------------------------------------------
 # Set location of GNUstep dirs for later use
-GNUSTEP_HDIR=$GNUSTEP_SYSTEM_ROOT/Headers
+GNUSTEP_HDIR=$GNUSTEP_SYSTEM_ROOT/Library/Headers
 if test "$GNUSTEP_FLATTENED" = yes; then
-  GNUSTEP_LDIR=$GNUSTEP_SYSTEM_ROOT/Libraries
+  GNUSTEP_LDIR=$GNUSTEP_SYSTEM_ROOT/Library/Libraries
 else
-  clean_target_os=`$GNUSTEP_SYSTEM_ROOT/Makefiles/clean_os.sh $target_os`
-  clean_target_cpu=`$GNUSTEP_SYSTEM_ROOT/Makefiles/clean_cpu.sh $target_cpu`
+  clean_target_os=`$GNUSTEP_MAKEFILES/clean_os.sh $target_os`
+  clean_target_cpu=`$GNUSTEP_MAKEFILES/clean_cpu.sh $target_cpu`
   obj_dir=$clean_target_cpu/$clean_target_os
-  GNUSTEP_LDIR=$GNUSTEP_SYSTEM_ROOT/Libraries/$obj_dir
+  GNUSTEP_LDIR=$GNUSTEP_SYSTEM_ROOT/Library/Libraries/$obj_dir
 fi
 CPPFLAGS="$CPPFLAGS -I$GNUSTEP_HDIR"
 LDFLAGS="$LDFLAGS -L$GNUSTEP_LDIR/$LIBRARY_COMBO -L$GNUSTEP_LDIR"
@@ -6761,7 +6754,7 @@ esac
 # Don't blindly perform a `cd "$ac_dir"/$ac_foo && pwd` since $ac_foo can be
 # absolute.
 ac_abs_builddir=`cd "$ac_dir" && cd $ac_builddir && pwd`
-ac_abs_top_builddir=`cd "$ac_dir" && cd ${ac_top_builddir}. && pwd`
+ac_abs_top_builddir=`cd "$ac_dir" && cd $ac_top_builddir && pwd`
 ac_abs_srcdir=`cd "$ac_dir" && cd $ac_srcdir && pwd`
 ac_abs_top_srcdir=`cd "$ac_dir" && cd $ac_top_srcdir && pwd`
 
diff --git a/configure.ac b/configure.ac
index e0e84d1..2f92f74 100644
--- a/configure.ac
+++ b/configure.ac
@@ -34,7 +34,7 @@ fi
 #--------------------------------------------------------------------
 # Use config.guess, config.sub and install-sh provided by gnustep-make
 #--------------------------------------------------------------------
-AC_CONFIG_AUX_DIR($GNUSTEP_SYSTEM_ROOT/Makefiles)
+AC_CONFIG_AUX_DIR($GNUSTEP_MAKEFILES)
 
 #--------------------------------------------------------------------
 # Determine the host, build, and target systems
@@ -47,14 +47,14 @@ AC_CANONICAL_TARGET([])
 # in the GNUstep root are used before the standard ones
 #--------------------------------------------------------------------
 # Set location of GNUstep dirs for later use
-GNUSTEP_HDIR=$GNUSTEP_SYSTEM_ROOT/Headers
+GNUSTEP_HDIR=$GNUSTEP_SYSTEM_ROOT/Library/Headers
 if test "$GNUSTEP_FLATTENED" = yes; then
-  GNUSTEP_LDIR=$GNUSTEP_SYSTEM_ROOT/Libraries
+  GNUSTEP_LDIR=$GNUSTEP_SYSTEM_ROOT/Library/Libraries
 else
-  clean_target_os=`$GNUSTEP_SYSTEM_ROOT/Makefiles/clean_os.sh $target_os`
-  clean_target_cpu=`$GNUSTEP_SYSTEM_ROOT/Makefiles/clean_cpu.sh $target_cpu`
+  clean_target_os=`$GNUSTEP_MAKEFILES/clean_os.sh $target_os`
+  clean_target_cpu=`$GNUSTEP_MAKEFILES/clean_cpu.sh $target_cpu`
   obj_dir=$clean_target_cpu/$clean_target_os
-  GNUSTEP_LDIR=$GNUSTEP_SYSTEM_ROOT/Libraries/$obj_dir
+  GNUSTEP_LDIR=$GNUSTEP_SYSTEM_ROOT/Library/Libraries/$obj_dir
 fi
 CPPFLAGS="$CPPFLAGS -I$GNUSTEP_HDIR"
 LDFLAGS="$LDFLAGS -L$GNUSTEP_LDIR/$LIBRARY_COMBO -L$GNUSTEP_LDIR"