Autoconf has always implicitly embedded the contents of confdefs.h at the top of every test program it compiles.  This behavior is at least 20 years old, probably even longer -- I think I remember autoconf 2.13 doing it.

Your code breaks with 2.69d because AC_USE_SYSTEM_EXTENSIONS defines more macros now, and that trips what appears to be a bug in GCC. Consider this test fragment:

#define ordinary_macro 1
#define ordinary_macro 1
#define __STDC_anything 1
#define __STDC_anything 1

Compiling with -Werror, I get a "macro __STDC_anything redefined" error with GCC 9 and 10, but I do not get a "macro ordinary_macro redefined" error.  With clang, I get no errors at all.  I've reported this as a bug in GCC: <https://gcc.gnu.org/bugzilla/show_bug.cgi?id=97998>.

> I wonder if 'confdefs.h' would benefit from '#ifndef / #define / #endif' guards.

This is a good idea but will not be possible for 2.70, because confdefs.h is built up over the course of the configure process, by appending to it with shell `>>`.  We would have to come up with a way to insert each new definition before the #endif.  I think this would be possible with clever use of `sed` but it would be too risky of a change for how close to the release we are.

I'm going to tag this bug to be revisited after the 2.70 release, when we may be able to make a change along the lines you suggest, and add something to the release notes about this problem.

Please be aware that running configure tests with -Werror in effect is not supported.  We cannot currently guarantee that the code generated for various tests will remain warning-free as C compilers continue to get pickier.  It's on the TODO list, but it's going to take major internal changes (for instance, the code generated by AC_CHECK_FUNC is just plain wrong, but we've been putting off a fix for decades because of how difficult it will be to fix it without breaking anything).

I'm not sure if it's a bug or feature. Filing a bug to clarify.

Initially bug is observed on apr-1.7.0 package: https://bugs.gentoo.org/750353

Here is a small example extracted from apr source code at https://github.com/apache/apr/blob/trunk/build/apr_common.m4#L508:

AC_PREREQ([2.59])

AC_INIT

dnl this seems to be the trigger:
AC_USE_SYSTEM_EXTENSIONS

CFLAGS="$CFLAGS -Werror"
AC_COMPILE_IFELSE(
  [AC_LANG_SOURCE(
   [#include "confdefs.h"
   int main(int argc, const char *const *argv) { return 0; }]
  )], [:], [AC_MSG_ERROR(Found warnings)])

AC_OUTPUT

Worked before as:

$ autoreconf-2.69 && ./configure --host=x86_64-pc-linux-gnu
checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
configure: creating ./config.status

OK.

Fails now:

$ autoreconf-2.69d && ./configure --host=x86_64-pc-linux-gnu
checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
checking for x86_64-pc-linux-gnu-gcc option to enable C11 features... none needed
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking whether _XOPEN_SOURCE should be defined... no
configure: error: Found warnings

config.log says it happens because now "confdefs.h" is already included in tests:

...
configure:3350: x86_64-pc-linux-gnu-gcc -c -g -O2 -Werror  conftest.c >&5
In file included from conftest.c:31:
confdefs.h:22: error: "__STDC_WANT_IEC_60559_ATTRIBS_EXT__" redefined [-Werror]
   22 | #define __STDC_WANT_IEC_60559_ATTRIBS_EXT__ 1
      |
...
cc1: all warnings being treated as errors
configure:3350: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define STDC_HEADERS 1
| #define __EXTENSIONS__ 1
| #define _ALL_SOURCE 1
| #define _DARWIN_C_SOURCE 1
| #define _GNU_SOURCE 1
| #define _POSIX_PTHREAD_SEMANTICS 1
| #define __STDC_WANT_IEC_60559_ATTRIBS_EXT__ 1
| #define __STDC_WANT_IEC_60559_BFP_EXT__ 1
| #define __STDC_WANT_IEC_60559_DFP_EXT__ 1
| #define __STDC_WANT_IEC_60559_FUNCS_EXT__ 1
| #define __STDC_WANT_IEC_60559_TYPES_EXT__ 1
| #define __STDC_WANT_LIB_EXT2__ 1
| #define __STDC_WANT_MATH_SPEC_FUNCS__ 1
| #define _TANDEM_SOURCE 1
| /* end confdefs.h.  */
| #include "confdefs.h"
|    int main(int argc, const char *const *argv) { return 0; }
|
configure:3354: error: Found warnings

I wonder if 'confdefs.h' would benefit from '#ifndef / #define / #endif' guards.

Thank you!