Stage#execute takes a Collection<Item<T>> parameter. I don't recall any case in which it has ever made sense for the items in that collection not to be treated as ordered. I know that a lot of the real-word use cases would fail if the ArrayList that underlies the current implementation was replaced by, say, a HashSet.
If we're actually assuming an ordered collection, we should probably make that explicit by changing that parameter to a List<Item<T>> instead.
This will obviously affect a lot of classes, although not as many as you might think (many are written as subclasses of a base class that implements the iteration, and operate only on a single item at a time). Nevertheless, to make a simpler transition for downstream packages, it might be worth seeing whether the old method signature can be changed to a deprecated default implementation which performs a cast and a deprecation warning. This is probably not absolutely required, as I think most of the affected classes not within the MDA itself will be in the ukf-mda and inc-mda projects, which are in my care in any case.