It's been pointed out on the GNU make lists that by including gnulib content we've effectively updated our minimum required compiler from C90 to C99.
That may be acceptable, but I think the gnulib docs (at least), if not gnulib-tool, should make clear that AC_PROG_CC_C99 (at least) needs to be added to to configure.ac. In GNU make we only have AC_PROG_CC which was fine before we started using gnulib but now causes failures on systems where this gives a C89 compiler, without extra options needed to choose C99. Gnulib macros may also need to fail the configure if the compiler cannot support C99.