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Refactor muxing workflow from single-pass to plan-execute model with stale-input checking, structural verification, and atomic output replacement. Add config migration, diagnostics export, background GUI jobs with progress tracking, and comprehensive integration tests. Improve safety with archive resource limits, font conflict detection, and shared resource cleanup coordination. Introduce new models (EpisodeIdentity, SourceTrackInfo, FileSnapshot, MuxPlanSnapshot) and rewrite matcher for global confidence assignment. Replace pymkv subprocess library use with direct mkvmerge -J JSON verification.
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