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Added tree-aware pairwise Mash distance evaluation with early-stop pruning ("prove > threshold") and persistent caching under <out_dir>/logs/ to avoid recomputation across repeated runs.
PlanUI: threshold modal (T) recomputes and reselects rounds; tree labels show Mash:…@source when the displayed distance originates from a descendant witness/max to avoid misinterpretation.
CLI: optional prompt before computing Mash distances (includes leaf / max-pairs estimate) and stronger warning when mash is missing; supports caching remote sequences up front so Mash can run locally.