paper-intake

name	paper-intake
description	Use when the user wants chat-only paper discovery, candidate summaries, direct arXiv URL/ID/arXiv DOI ingest, or natural paper names resolved before capture.

Paper Intake

Overview

Move papers from discovery to raw evidence without passing unresolved names to capture. The visible path is chat-only discovery -> raw/evidence/ -> wiki/papers/. For read/index work, consult docs/qmd-cli.md and runtime qmd --help.

Available Tools

Tool	Purpose
discover_papers	Search, score, deduplicate, and return transient candidates for chat presentation
ingest_and_read	Capture one or many resolved arXiv URLs, IDs, or arXiv DOI values
upsert_wiki_page	Create canonical paper pages after reading and distilling
check_concept_alias	Resolve uncertain concept names before creating core concept pages

Routing Decision

Execute this decision tree before any tool call:

1. User asked for discovery without asking to ingest specific papers: call discover_papers(query=...), present returned candidates in chat, apply the agent-side presentation guidance in references/post-discovery-rescoring.md, then stop.
2. User selects a candidate from the current conversation: resolve that candidate to an arXiv URL, arXiv ID, or arXiv DOI value, then call ingest_and_read(input_value=...).
3. User provided arXiv URL(s), arXiv ID(s), or arXiv DOI value(s): call ingest_and_read(input_value=...) directly. Batch multiple resolved identifiers into one call when possible.
4. User provided title(s), acronym(s), alias(es), project name(s), or mixed natural paper references: resolve each reference to an arXiv URL, ID, or arXiv DOI value first, then call ingest_and_read with only the resolved identities. Do not pass unresolved names to MCP.
5. User asked whether something is already in the vault or wants to read local evidence: use QMD CLI directly, usually qmd query or qmd get.
6. User wants a canonical paper page after capture and reading: hand off to the paper-distillation skill.

Core Rules

• Discovery is chat-only. Treat discover_papers results as transient candidates. Present them in chat and stop unless the user also gave a specific resolved identity to capture.
• Ingest captures only resolved identities. ingest_and_read accepts arXiv URLs, arXiv IDs, and arXiv DOI values. Natural references are agent-resolved before the MCP call. Do not edit raw/evidence/ by hand. See references/ingest-rules.md for the resolved/unresolved reporting contract and capture repair behavior.
• Canonical pages are a separate skill. Distillation from raw/evidence/ to wiki/papers/ is handled by the paper-distillation skill. The canonical flow requires 1–5 concepts in key_concepts_topk, at least one wikilinked in the body, and check_concept_alias before linking uncertain concept surfaces.
• Conversation insights use the tool path. If a paper-intake conversation surfaces a durable insight about why a paper matters, save the distilled takeaway to insights/conversations/ through the Python write path. Do not save verbatim transcripts or edit insight files by hand.

Post-Discovery Re-scoring

After discover_papers returns, the agent should review returned low-score candidates against the user's research_profile.direction before presenting results. Promote semantically relevant candidates in the chat summary with a one-line reason. See references/post-discovery-rescoring.md for the full playbook.

QMD CLI Guidance

• Use QMD CLI directly for qmd query, qmd get, qmd status, qmd update, qmd embed -f, and collection/context health.
• Check docs/qmd-cli.md first for the Paper Distill mapping.
• If command details are uncertain, follow runtime qmd --help.

Output Expectations

• After discovery, summarize the strongest candidates, include resolved arXiv identities or arXiv DOI values when available, and stop for user selection.
• After ingest, report exact identifiers processed and unresolved references separately.
• If ingest cannot proceed, explain the blocking state in one sentence before suggesting the next step.

Skill / Tool Contract

This skill is responsible for intent routing, resolved-identity discipline, summarizing outcomes, and suggesting the next useful action.

Python tools are responsible for deterministic I/O, path safety, capture, and structured errors.