Decouple qualified/unqualified from including subdirectories

As discussed in today's meeting:

Right now, the qualified/unqualified choice is for all languages and this is a problem. This problem was revealed for Coq, since Coq uses the qualified semantic and OCaml only supports the unqualified one. And even if OCaml supported both, we might want different settings for Coq and OCaml when extracting OCaml code from Coq.

In the end, we agreed that for most language the choice is made once and for all by the language itself. It is only for OCaml where the user can make this choice. So in the end we decided to de-couple both settings. include_subdirs will now have two state: true and false, and in the true case we can additionally specify whether OCaml sources are qualified or not. For instance:

(include_subdirs true (ocaml unqualified))

We should add the new syntax and deprecated the old one. In version 3 of the language, we'll forbid the old syntax.

Start at the existing include_subdirs syntax and the qualified/unqualified configuration handling described in the issue. Trace how both settings are parsed and validated for OCaml and other languages. Done means the new nested syntax is accepted, the old syntax is deprecated, and version 3 rejects the old syntax.