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name: papi description: Help with paper references using paperpipe (papi). Use when user asks about papers, wants to verify code against a paper, needs paper context for implementation, or asks about equations/methods from literature. allowed-tools: Read, Bash, Glob, Grep

Paper Reference Assistant

Use when user mentions papers, arXiv IDs, equations, or "does this match the paper?"

Setup

Copypapi path   # DB location (default ~/.paperpipe/; override via PAPER_DB_PATH)
papi list   # available papers

Decision Rules (Cheapest First)

1. papi show <paper> -l eq|tex|summary — prints to stdout
2. MCP tools for "top passages about X":
   • leann_search(index_name, query, top_k) — fast, returns snippets
   • retrieve_chunks(query, index_name, k) — slower, formal citations
   • Check indexes: leann_list() or list_pqa_indexes()
   • Embedding priority: Voyage AI → Google/Gemini → OpenAI → Ollama
3. papi ask — only when user explicitly requests RAG synthesis

Code Verification

1. papi show {name} -l eq — compare symbols with implementation
2. papi show {name} -l tex — exact definitions if ambiguous
3. papi notes {name} — implementation gotchas

Implementation Guidance

1. papi show {name} -l summary — high-level approach
2. papi show {name} -l eq — formulas to implement

Cross-Paper Search

Copypapi search --rg "query"              # exact text (fast, no LLM)
papi search --rg --regex "pattern"    # regex (OR, wildcards)
papi search "query"                   # ranked BM25
papi search --hybrid "query"          # ranked + exact boost
papi ask "question"                   # PaperQA2 RAG
papi ask "question" --backend leann   # LEANN RAG

Adding Papers

Copypapi add 2303.13476                   # arXiv ID
papi add https://arxiv.org/abs/...    # URL
papi add --pdf /path/to.pdf           # local PDF
papi add --pdf "https://..."          # PDF from URL
papi add --from-file papers.bib       # bulk import

Per-Paper Files

Located at {db}/papers/{name}/:

If agent can't read ~/.paperpipe/, export to repo: papi export <papers...> --level equations --to ./paper-context/ Use --figures to include extracted figures in export.

See commands.md for full reference.