Sorry if this is a faq, but I have found nothing convincing, excepted this unanswered message:
http://sourceware.org/ml/bug-automake/2001/msg00391.html and http://sources.redhat.com/ml/bug-automake/2003/msg00311.html where adl seems to agree it should be cleaned. I don't understand why make clean should not clean EXTRA_PROGRAMS. I agree EXTRA_PROGRAMS is not hooked on "all", so it makes some sense not to attach it to "clean". In fact, Tom extended extra.test in 1996 to include an explicit check that it is not: http://sources.redhat.com/cgi-bin/cvsweb.cgi/automake/tests/extra.test?annotate=1.2&cvsroot=automake But I find this inconvenient. The documentation should at least warn the user about this. Maybe Tom has an opinion about this?