BUILD_EXEEXT was not properly set (config macro AX_PROG_CC_FOR_BUILD).
Apparently we need aclocal/automake version 1.13 or higher and to
distribute ax_prog_cc_for_build.m4 ourselves to benefit from a fix
released only in autoconf 2.69.
Thanks to Éric Hoffman for reporting and investigating on this.
Automake 1.13 apparently dates from 2012 and debian testing provides
a newer version (automake 1.15) so it should be ok to update it. Also
that's only a build dependency.
Jehan