5.3.2.3 Subdirectories with AC_SUBST

Another possibility is to define MAYBE_OPT from ./configure using AC_SUBST (see Setting Output Variables).

…
if test "$want_opt" = yes; then
  MAYBE_OPT=opt
else
  MAYBE_OPT=
fi
AC_SUBST([MAYBE_OPT])
AC_CONFIG_FILES([Makefile src/Makefile opt/Makefile])
…

In this case the top-level Makefile.am should look as follows.

SUBDIRS = src $(MAYBE_OPT)
DIST_SUBDIRS = src opt

The drawback of this method is that since Automake cannot guess what the possible values of MAYBE_OPT are, it is necessary to define DIST_SUBDIRS.