FYI, I solved this problem by letting gnulib put GNUmakefile and maint.mk into build-aux/, and use this top-level GNUmakefile:
have-gnulib-files := $(shell test -f gnulib.mk && test -f maint.mk && echo yes) ifneq ($(have-gnulib-files),yes) gnulib.mk: ln -s build-aux/GNUmakefile gnulib.mk || cp build-aux/GNUmakefile gnulib.mk ln -s build-aux/maint.mk maint.mk || cp build-aux/maint.mk maint.mk endif -include gnulib.mk If this approach works out well, it should go into the manual, because without it, the maintainer-makefile module seems useless for projects that use AC_CONFIG_AUX_DIR. /Simon