Why is ./configure ignoring subdirectories? [duplicate]
It's not something you add "case-by-case", as AUTOMAKE_OPTIONS applies to the whole project. It's also supposedly the only way it should be used in the future, thus the warnings; for now it's opt-in.
You can also set this in configure.ac with AM_INIT_AUTOMAKE, see Autotools Mythbuster (full disclosure: I'm the author) for the full set of automake options you can use.