7.2.2 Subdirectories with AM_CONDITIONAL

configure should output the Makefile for each directory and define a condition into which opt/ should be built.

     ...
     AM_CONDITIONAL([COND_OPT], [test "$want_opt" = yes])
     AC_CONFIG_FILES([Makefile src/Makefile opt/Makefile])
     ...

Then SUBDIRS can be defined in the top-level Makefile.am as follows.

     if COND_OPT
       MAYBE_OPT = opt
     endif
     SUBDIRS = src $(MAYBE_OPT)

As you can see, running make will rightly recurse into src/ and maybe opt/.

As you can't see, running ‘make dist’ will recurse into both src/ and opt/ directories because ‘make dist’, unlike ‘make all’, doesn't use the SUBDIRS variable. It uses the DIST_SUBDIRS variable.

In this case Automake will define ‘DIST_SUBDIRS = src opt’ automatically because it knows that MAYBE_OPT can contain ‘opt’ in some condition.