Critical gaps across all dimensions. Tool descriptions range from adequate to vague; most lack actionable context for LLM selection. Input schemas present but sparse, many parameters lack type constraints and descriptions. No output schemas documented. Error handling absent. Tool names lack clear action verbs (e.g., 'queue_manager' is a noun, not verb_noun). No parameter validation guidance. Security concerns: queue_manager and paperreview tools accept file paths without sanitization hints. Composition issues: tools operate on disparate domains (experiment scheduling, figure rendering, paper review, proteomics) with no clear chaining. Per-tool scores: build_manifest=38, queue_manager=28, figure_renderer=35, validate_spec=32, paperreview_submit_and_wait=35, paperreview_render=30, analyze_region_proteome=18.

• Rename tools to verb_noun pattern: 'queue_manager' → 'manage_experiment_queue', 'figure_renderer' → 'render_figure_spec', 'validate_spec' → 'validate_figure_spec'. This clarifies intent and aids LLM selection.
• Document output schemas for all tools. E.g., build_manifest returns {manifest: {project, cwd, phases: [{name, jobs: [{id, cmd, expected_output}]}]}}. Include field types and descriptions.
• Add parameter descriptions for all inputs. E.g., 'config' → 'Path to YAML or JSON grid specification file (must exist, readable, <10MB)'. Include format constraints and examples.
• Add error handling guidance to descriptions. E.g., queue_manager: 'Retryable on GPU unavailability; fatal on manifest parse error. Returns {status, error_code, recovery_hint}.'
• Implement input validation and return actionable errors. E.g., 'Invalid manifest path: /nonexistent/file.json, file does not exist. Check path and permissions.' instead of generic exceptions.