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7.2.3 Subdirectories with AC_SUBST

Another possibility is to define MAYBE_OPT from ./configure using AC_SUBST: 

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