This note is meant to bring a shortcoming of -no-alias-deps to the attention of the rest of the developers, even if the beheaviour makes sense (as far as I understand module aliases). This flag, and module aliases, are used by Dune to implement wrapping of libraries and executables (see ocaml/dune#6820 for a related issue over at the Dune issue tracker).

Consider a file foo.ml with contents:

[@@@alert deprecated "Do not use this module."]
let x = 12

and a file main.ml with contents:

module F = Foo
let _ = Foo.x
let _ = F.x

Compile with:

$ ocamlc -c foo.ml
$ ocamlc -no-alias-deps -c main.ml
File "main.ml", line 2, characters 8-13:
2 | let _ = Foo.x
            ^^^^^
Alert deprecated: module Foo
Do not use this module.

and note that no alert is triggered for F.x which goes through the module alias.