Dead references after deep destructive substitutions

[Octachron]

When substituting a signature item inside a submodule

module type S = sig
  module M: sig
    type t
  end
  type t = M.t
end
module type T = S with type M.t := int

the reference to the submodule item M.t are not updated outside of the submodule, which creates a dead reference inside the module type u.