It looks like modifying include/hwloc/config.h.in (the one *not* generated by autoheader) does not cause the build to re-run configure so as to regenerate include/hwloc/config.h
One solution is AC_SUBST(CONFIG_STATUS_DEPENDENCIES, '$(top_srcdir)/include/hwloc/config.h.in <and maybe others .in files>') But I wonder why the autotools do not take care of this automagically. Brice