• Per-collection search stores keep semantic indexes portable.
• Deletion guard avoids destructive surprises in watch mode; suppressed deletions surface as notes/JSON.
• CLI helpers centralize quiet/summary/JSON behavior and standardized error payloads.
• Lazy CLI imports keep startup snappy and improve testability.
• Persistent document_ids allow stable references across rename/move/undo flows.

See ARCH.md and SPEC.md for deeper rationale and trade-offs.