Clear all wrote `/Annots []` on a page that had no annotations and replaced
an indirect `/Annots` array with an inline copy. It also left replies to a
mark in place, so their `/IRT` kept the cleared mark in the document (and in
the comment list, as a reply to nothing).
`clear_marks` now writes the list through the annot crate's `set_annots`
(made public), as deleting a comment does, and removes each mark's replies
and pop-ups with it. The "what goes with a deleted comment" walk moves from
`delete_annotation` into `with_replies_and_popups`, which both use; it visits
each annotation once instead of sweeping the list until nothing changes.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>