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Follow-up to #2532 (review by aiongg): the structure-tree walk started only at the root's /K, so an element listed only in /ParentTree or /IDTree kept its object reference to a removed link or comment, and the root kept that annotation reachable in a full rewrite. The walk now also starts from both trees and follows their nodes (/Nums, /Names, /Kids), written in place or as their own objects. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Gv2WwdgjmBz33GWkwgNn3Q