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Scored across 5 tools
The mutation tools (mark_processed, clear_processed) and their read counterparts are clearly distinct. However, get_reading_context already bundles the front document, its pending underlines, and page info, which overlaps with get_pending_underlines and get_open_documents, so an agent may be unsure when to call the narrow getters versus the aggregate.
All names use snake_case with a verb-first, noun-object pattern (get_/mark_/clear_ + resource). The verb variation is semantically meaningful (reads vs. state mutations) rather than inconsistent.
Five tools is well-scoped for a Skim reading-support server: two read getters, one aggregate context call, and two annotation-state mutations. Every tool earns its place with no filler.
The pending-red → gray → deleted lifecycle is fully covered, plus document listing and rich reading context. The main gap is the absence of an inverse to mark_processed (no way to revert gray back to red) or any annotation-creation ability, though the core workflow is complete.