When AC_SYSTEM_EXTENSIONS precedes AM_INIT_AUTOMAKE, it used to throw an error - which has been fixed in http://debbugs.gnu.org/cgi/bugreport.cgi?bug=15981 .
I have here another instance of what appears to be a similar issue. This one is also a regression (used to work in 1.13.4), and the regression is still present in {automake 1.14.1 + patch from #15981}. The problem originates in libmemcached/configure.ac, and I have produced the following reduced testcase that exhibits the issue: $ cat <<EOF >configure.ac AC_INIT([foo], [0]) AC_PROG_CC([cc gcc clang]) AC_CONFIG_AUX_DIR([build-aux]) AC_CONFIG_MACRO_DIR([m4]) AM_INIT_AUTOMAKE([1.11 subdir-objects foreign]) AC_OUTPUT([Makefile]) EOF $ echo '' >Makefile.am $ md m4 $ autoreconf -fi configure.ac:2: installing 'build-aux/compile' configure.ac:5: installing 'build-aux/install-sh' configure.ac:5: installing 'build-aux/missing' $ ./configure checking for cc... cc 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 cc accepts -g... yes checking for cc option to accept ISO C89... none needed configure: error: cannot find install-sh, install.sh, or shtool in "." "./.." "./../.." With automake-1.13.4, configure would succeed through to the end ("config.status: creating Makefile").