- Remove Theme System sections (removed in ADR-0013) - Delete stale THEMING.md (283 lines documenting removed system) - Remove Favorites from sidebar (removed in codebase) - Remove Closed Tab History section (single note model, ADR-0003) - Fix commands.rs → commands/ (split into modules) - Remove stale config/relations.md and config/semantic-properties.md refs - Fix protected folders list (remove _themes/, theme/) Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>