Paper Graph

Build a Markdown report with embedded Mermaid diagrams showing how research on a user-specified topic (or paper) evolved — clustered into challenges → solutions and traced as per-solution evolution paths.

The skill has no outbound LLM dependency. The host agent provides all LLM calls; the skill provides deterministic data fetchers (S2 / DeepXiv), prompt templates, markdown parsers, and Mermaid renderers. Run the runbook below step-by-step.

Execution requirement. When the caller already provides parsed_query.json, seed.json and papers.json (wherever they are, for example in an input/ directory), copy them into the workdir under those names, treat steps 1–5 as complete and start at step 6. Still run every deterministic CLI step from classify through assemble; do not replace parsing, edge audit, rendering, or assembly with hand-authored Mermaid. Before finishing, verify that every parsed solution has a detail render and an audit verdict file, even when that file is an empty JSON list. Treat assemble_report as the only final-report writer: do not edit or append hand-authored edges afterward, even when a caller asks to display uncertain relationships. Preserve uncertainty in verdict JSON.

When to Use This Skill

Trigger when the user asks something like:

• "Show me the history of " / "How did evolve?"
• "Where does stem from?" / "What did build on?"
• "What are significant improvements / follow-ups to ?"
• "Trace the lineage of ideas in " / "Give me a literature taxonomy of "
• "Citation tree of " / "Idea trace of "