`@all` target doesn't interact well with `(include_subdirs ...)`

[ejgallego]

As witnessed by #1968 , targets that are generated by subdirs are not included in the @all alias.

[rgrinberg]

This line in gen_rules.ml is the one that causes the issue:

    Build_system.Alias.add_deps
      ~dyn_deps
      (Build_system.Alias.all ~dir:ctx_dir) Path.Set.empty;

It assumes that all targets that are created by a stanza live inside the directory which contains the stanza. The case where we have subdirs means that some targets live in subdirectories so we should be a little smarter here.

[anmonteiro]

related: #12628