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/usr/src/gcc-4.9/debian/patches/gcc-sysroot.diff is in gcc-4.9-source 4.9.3-13ubuntu2.

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# DP: Allow building --with-sysroot=/

Index: b/src/gcc/configure.ac
===================================================================
--- a/src/gcc/configure.ac
+++ b/src/gcc/configure.ac
@@ -117,6 +117,69 @@
 	local_prefix=/usr/local
 fi
 
+AC_ARG_WITH([native-system-header-dir],
+  [  --with-native-system-header-dir=dir
+                          use dir as the directory to look for standard
+                          system header files in.  Defaults to /usr/include.],
+[
+ case ${with_native_system_header_dir} in
+ yes|no) AC_MSG_ERROR([bad value ${withval} given for --with-native-system-header-dir]) ;;
+ /* | [[A-Za-z]]:[[\\/]]*) ;;
+ *) AC_MSG_ERROR([--with-native-system-header-dir argument ${withval} must be an absolute directory]) ;;
+ esac
+ configured_native_system_header_dir="${withval}"
+], [configured_native_system_header_dir=])
+
+AC_ARG_WITH(build-sysroot, 
+  [AS_HELP_STRING([--with-build-sysroot=sysroot],
+                  [use sysroot as the system root during the build])],
+  [if test x"$withval" != x ; then
+     SYSROOT_CFLAGS_FOR_TARGET="--sysroot=$withval"
+   fi],
+  [SYSROOT_CFLAGS_FOR_TARGET=])
+AC_SUBST(SYSROOT_CFLAGS_FOR_TARGET)
+
+if test "x$prefix" = xNONE; then
+ test_prefix=/usr/local
+else
+ test_prefix=$prefix
+fi
+if test "x$exec_prefix" = xNONE; then
+ test_exec_prefix=$test_prefix
+else
+ test_exec_prefix=$exec_prefix
+fi
+
+AC_ARG_WITH(sysroot,
+[AS_HELP_STRING([[--with-sysroot[=DIR]]],
+		[search for usr/lib, usr/include, et al, within DIR])],
+[
+ case ${with_sysroot} in
+ yes) TARGET_SYSTEM_ROOT='${exec_prefix}/${target_noncanonical}/sys-root' ;;
+ *) TARGET_SYSTEM_ROOT=$with_sysroot ;;
+ esac
+   
+ TARGET_SYSTEM_ROOT_DEFINE='-DTARGET_SYSTEM_ROOT=\"$(TARGET_SYSTEM_ROOT)\"'
+ CROSS_SYSTEM_HEADER_DIR='$(TARGET_SYSTEM_ROOT)$${sysroot_headers_suffix}$(NATIVE_SYSTEM_HEADER_DIR)'
+	
+ case ${TARGET_SYSTEM_ROOT} in
+ "${test_prefix}"|"${test_prefix}/"*|\
+ "${test_exec_prefix}"|"${test_exec_prefix}/"*|\
+ '${prefix}'|'${prefix}/'*|\
+ '${exec_prefix}'|'${exec_prefix}/'*)
+   t="$TARGET_SYSTEM_ROOT_DEFINE -DTARGET_SYSTEM_ROOT_RELOCATABLE"
+   TARGET_SYSTEM_ROOT_DEFINE="$t"
+   ;;
+ esac
+], [
+ TARGET_SYSTEM_ROOT=
+ TARGET_SYSTEM_ROOT_DEFINE=
+ CROSS_SYSTEM_HEADER_DIR='$(gcc_tooldir)/sys-include'
+])
+AC_SUBST(TARGET_SYSTEM_ROOT)
+AC_SUBST(TARGET_SYSTEM_ROOT_DEFINE)
+AC_SUBST(CROSS_SYSTEM_HEADER_DIR)
+
 # Don't set gcc_gxx_include_dir to gxx_include_dir since that's only
 # passed in by the toplevel make and thus we'd get different behavior
 # depending on where we built the sources.
@@ -148,7 +211,9 @@
 if test "${with_sysroot+set}" = set; then
   gcc_gxx_without_sysroot=`expr "${gcc_gxx_include_dir}" : "${with_sysroot}"'\(.*\)'`
   if test "${gcc_gxx_without_sysroot}"; then
-    gcc_gxx_include_dir="${gcc_gxx_without_sysroot}"
+    if test x${with_sysroot} != x/; then
+      gcc_gxx_include_dir="${gcc_gxx_without_sysroot}"
+    fi
     gcc_gxx_include_dir_add_sysroot=1
   fi
 fi
@@ -738,69 +803,6 @@
 ], [enable_shared=yes])
 AC_SUBST(enable_shared)
 
-AC_ARG_WITH([native-system-header-dir],
-  [  --with-native-system-header-dir=dir
-                          use dir as the directory to look for standard
-                          system header files in.  Defaults to /usr/include.],
-[
- case ${with_native_system_header_dir} in
- yes|no) AC_MSG_ERROR([bad value ${withval} given for --with-native-system-header-dir]) ;;
- /* | [[A-Za-z]]:[[\\/]]*) ;;
- *) AC_MSG_ERROR([--with-native-system-header-dir argument ${withval} must be an absolute directory]) ;;
- esac
- configured_native_system_header_dir="${withval}"
-], [configured_native_system_header_dir=])
-
-AC_ARG_WITH(build-sysroot, 
-  [AS_HELP_STRING([--with-build-sysroot=sysroot],
-                  [use sysroot as the system root during the build])],
-  [if test x"$withval" != x ; then
-     SYSROOT_CFLAGS_FOR_TARGET="--sysroot=$withval"
-   fi],
-  [SYSROOT_CFLAGS_FOR_TARGET=])
-AC_SUBST(SYSROOT_CFLAGS_FOR_TARGET)
-
-if test "x$prefix" = xNONE; then
- test_prefix=/usr/local
-else
- test_prefix=$prefix
-fi
-if test "x$exec_prefix" = xNONE; then
- test_exec_prefix=$test_prefix
-else
- test_exec_prefix=$exec_prefix
-fi
-
-AC_ARG_WITH(sysroot,
-[AS_HELP_STRING([[--with-sysroot[=DIR]]],
-		[search for usr/lib, usr/include, et al, within DIR])],
-[
- case ${with_sysroot} in
- yes) TARGET_SYSTEM_ROOT='${exec_prefix}/${target_noncanonical}/sys-root' ;;
- *) TARGET_SYSTEM_ROOT=$with_sysroot ;;
- esac
-   
- TARGET_SYSTEM_ROOT_DEFINE='-DTARGET_SYSTEM_ROOT=\"$(TARGET_SYSTEM_ROOT)\"'
- CROSS_SYSTEM_HEADER_DIR='$(TARGET_SYSTEM_ROOT)$${sysroot_headers_suffix}$(NATIVE_SYSTEM_HEADER_DIR)'
-	
- case ${TARGET_SYSTEM_ROOT} in
- "${test_prefix}"|"${test_prefix}/"*|\
- "${test_exec_prefix}"|"${test_exec_prefix}/"*|\
- '${prefix}'|'${prefix}/'*|\
- '${exec_prefix}'|'${exec_prefix}/'*)
-   t="$TARGET_SYSTEM_ROOT_DEFINE -DTARGET_SYSTEM_ROOT_RELOCATABLE"
-   TARGET_SYSTEM_ROOT_DEFINE="$t"
-   ;;
- esac
-], [
- TARGET_SYSTEM_ROOT=
- TARGET_SYSTEM_ROOT_DEFINE=
- CROSS_SYSTEM_HEADER_DIR='$(gcc_tooldir)/sys-include'
-])
-AC_SUBST(TARGET_SYSTEM_ROOT)
-AC_SUBST(TARGET_SYSTEM_ROOT_DEFINE)
-AC_SUBST(CROSS_SYSTEM_HEADER_DIR)
-
 AC_ARG_WITH(specs,
   [AS_HELP_STRING([--with-specs=SPECS],
                   [add SPECS to driver command-line processing])],