---

name: research-lit description: Search and analyze research papers, find related work, summarize key ideas. Use when user says "find papers", "related work", "literature review", "what does this paper say", or needs to understand academic papers. argument-hint: "[paper-topic-or-url]" allowed-tools: Bash(), Read, Glob, Grep, WebSearch, WebFetch, Write, Agent, mcp__zotero__, mcp__obsidian-vault__*

Research Literature Review

Research topic: $ARGUMENTS

Constants

• PAPER_LIBRARY — Local directory containing user's paper collection (PDFs). Check these paths in order:
  1. papers/ in the current project directory
  2. literature/ in the current project directory
  3. Custom path specified by user in CLAUDE.md under ## Paper Library
• MAX_LOCAL_PAPERS = 20 — Maximum number of local PDFs to scan (read first 3 pages each). If more are found, prioritize by filename relevance to the topic.
• SOURCES = all — Which literature sources to search. Options: zotero, obsidian, local, web, semantic-scholar, deepxiv, exa, gemini, openalex, all. Full source table and selection rules: see ## Data Sources below.
• ARXIV_DOWNLOAD = false — When true, download top 3-5 most relevant arXiv PDFs to PAPER_LIBRARY after search. When false (default), only fetch metadata (title, abstract, authors) via arXiv API — no files are downloaded.
• ARXIV_MAX_DOWNLOAD = 5 — Maximum number of PDFs to download when ARXIV_DOWNLOAD = true.

💡 Overrides:

• /research-lit "topic" — paper library: ~/my_papers/ — custom local PDF path
• /research-lit "topic" — sources: zotero, local — only search Zotero + local PDFs
• /research-lit "topic" — sources: web — only search the web (skip all local)
• /research-lit "topic" — sources: web, semantic-scholar — also search Semantic Scholar for published venue papers (IEEE, ACM, etc.)
• /research-lit "topic" — sources: all, deepxiv — use default sources plus DeepXiv
• /research-lit "topic" — arxiv download: true — download top relevant arXiv PDFs
• /research-lit "topic" — arxiv download: true, max download: 10 — download up to 10 PDFs

Data Sources

This skill checks multiple sources in priority order. All are optional — if a source is not configured or not requested, skip it silently.

Source Selection

Parse $ARGUMENTS for a — sources: directive:

• If — sources: is specified: Only search the listed sources (comma-separated). Valid values: zotero, obsidian, local, web, semantic-scholar, deepxiv, exa, gemini, openalex, all.
• If not specified: Default to all — search every available source in priority order (semantic-scholar, deepxiv, exa, gemini, and openalex are excluded from all; they must be explicitly listed).

Examples:

/research-lit "diffusion models"                                    → all (default, no S2)
/research-lit "diffusion models" — sources: all                     → all (default, no S2)
/research-lit "diffusion models" — sources: zotero                  → Zotero only
/research-lit "diffusion models" — sources: zotero, web             → Zotero + web
/research-lit "diffusion models" — sources: local                   → local PDFs only
/research-lit "topic" — sources: obsidian, local, web               → skip Zotero
/research-lit "topic" — sources: web, semantic-scholar              → web + S2 API (IEEE/ACM venue papers)
/research-lit "topic" — sources: deepxiv                            → DeepXiv only
/research-lit "topic" — sources: all, deepxiv                       → default sources + DeepXiv
/research-lit "topic" — sources: all, semantic-scholar              → all + S2 API
/research-lit "topic" — sources: exa                               → Exa only (broad web + content extraction)
/research-lit "topic" — sources: all, exa                          → default sources + Exa web search
/research-lit "topic" — sources: gemini                            → Gemini only (AI-powered broad discovery)
/research-lit "topic" — sources: all, gemini                       → default sources + Gemini discovery
/research-lit "topic" — sources: gemini, semantic-scholar           → Gemini + S2 (broad discovery + venue metadata)
/research-lit "topic" — sources: openalex                          → OpenAlex only (open citation graph + institutions)
/research-lit "topic" — sources: semantic-scholar, openalex         → S2 + OpenAlex (complementary metadata)

Source Table

| Priority | Source | ID | How to detect | What it provides | |----------|--------|----|---------------|-----------------| | 1 | Zotero (via MCP) | zotero | Try calling any mcp__zotero__* tool — if unavailable, skip | Collections, tags, annotations, PDF highlights, BibTeX, semantic search | | 2 | Obsidian (via MCP) | obsidian | Try calling any mcp__obsidian-vault__* tool — if unavailable, skip | Research notes, paper summaries, tagged references, wikilinks | | 3 | Local PDFs | local | Glob: papers/**/*.pdf, literature/**/*.pdf | Raw PDF content (first 3 pages) | | 4 | Web search | web | Always available (WebSearch) | arXiv, Semantic Scholar, Google Scholar | | 5 | Semantic Scholar API | semantic-scholar | $S2_FETCHER resolves (canonical name semantic_scholar_fetch.py, per integration-contract §2) | Published venue papers (IEEE, ACM, Springer) with structured metadata: citation counts, venue info, TLDR. Only runs when explicitly requested via — sources: semantic-scholar or — sources: web, semantic-scholar | | 6 | DeepXiv CLI | deepxiv | $DEEPXIV_FETCHER resolves (canonical name deepxiv_fetch.py, per integration-contract §2) and deepxiv CLI present (command -v deepxiv) | Progressive paper retrieval: search, brief, head, section, trending, web search. Only runs when explicitly requested via — sources: deepxiv or — sources: all, deepxiv | | 7 | Exa Search | exa | $EXA_FETCHER resolves (canonical name exa_search.py, per integration-contract §2); fetcher handles exa-py SDK + API key internally | AI-powered broad web search with content extraction (highlights, text, summaries). Covers blogs, docs, news, companies, and research papers beyond arXiv/S2. Only runs when explicitly requested via — sources: exa or — sources: all, exa | | 8 | Gemini (MCP / CLI) | gemini | mcp__gemini-cli__ask-gemini tool available, or gemini CLI installed | AI-powered broad literature discovery — decomposes topics into sub-problems, aliases, and variants for wider retrieval. Prefers MCP, falls back to CLI. Only runs when explicitly requested via — sources: gemini or — sources: all, gemini | | 9 | OpenAlex | openalex | $OPENALEX_FETCHER resolves (canonical name openalex_fetch.py, per integration-contract §2) and Python requests module importable | Open citation graph with institutional affiliations, funding data, and comprehensive metadata across 250M+ works. Fully open API. Only runs when explicitly requested via — sources: openalex or — sources: all, openalex |

Graceful degradation: If no MCP servers are configured, the skill works exactly as before (local PDFs + web search). Zotero and Obsidian are pure additions.

Workflow

Step 0a: Search Zotero Library (if available)

Skip this step entirely if Zotero MCP is not configured.

Try calling a Zotero MCP tool (e.g., search). If it succeeds:

1. Search by topic: Use the Zotero search tool to find papers matching the research topic
2. Read collections: Check if the user has a relevant collection/folder for this topic
3. Extract annotations: For highly relevant papers, pull PDF highlights and notes — these represent what the user found important
4. Export BibTeX: Get citation data for relevant papers (useful for /paper-write later)
5. Compile results: For each relevant Zotero entry, extract:
   • Title, authors, year, venue
   • User's annotations/highlights (if any)
   • Tags the user assigned
   • Which collection it belongs to

📚 Zotero annotations are gold — they show what the user personally highlighted as important, which is far more valuable than generic summaries.

Step 0b: Search Obsidian Vault (if available)

Skip this step entirely if Obsidian MCP is not configured.

Try calling an Obsidian MCP tool (e.g., search). If it succeeds:

1. Search vault: Search for notes related to the research topic
2. Check tags: Look for notes tagged with relevant topics (e.g., #diffusion-models, #paper-review)
3. Read research notes: For relevant notes, extract the user's own summaries and insights
4. Follow links: If notes link to other relevant notes (wikilinks), follow them for additional context
5. Compile results: For each relevant note:
   • Note title and path
   • User's summary/insights
   • Links to other notes (research graph)
   • Any frontmatter metadata (paper URL, status, rating)

📝 Obsidian notes represent the user's processed understanding — more valuable than raw paper content for understanding their perspective.

Step 0c: Scan Local Paper Library

Before searching online, check if the user already has relevant papers locally:

1. Locate library: Check PAPER_LIBRARY paths for PDF files

   Glob: papers/**/*.pdf, literature/**/*.pdf
   

2. De-duplicate against Zotero: If Step 0a found papers, skip any local PDFs already covered by Zotero results (match by filename or title).

3. Filter by relevance: Match filenames and first-page content against the research topic. Skip clearly unrelated papers.

4. Summarize relevant papers: For each relevant local PDF (up to MAX_LOCAL_PAPERS):

   • Read first 3 pages (title, abstract, intro)
   • Extract: title, authors, year, core contribution, relevance to topic
   • Flag papers that are directly related vs tangentially related

5. Build local knowledge base: Compile summaries into a "papers you already have" section. This becomes the starting point — external search fills the gaps.

📚 If the user has a comprehensive local collection, the external search can be more targeted (focus on what's missing).

⚠️ If all three PAPER_LIBRARY paths miss, say so before moving on — do not skip silently. A user whose PDFs live in a reference manager (Zotero, Mendeley, ...) otherwise assumes — sources: all covered them. Emit:

WARN: local contributed nothing — no PDFs found in papers/, literature/, or a configured paper library. To include yours, add a "## Paper Library" heading to CLAUDE.md followed by the directory path.

Then continue to Step 1.

Step 1: Search (external)

• Use WebSearch to find recent papers on the topic
• Check arXiv, Semantic Scholar, Google Scholar
• Focus on papers from last 2 years unless studying foundational work
• De-duplicate: Skip papers already found in Zotero, Obsidian, or local library

arXiv API search (runs when — sources: is unset, contains web or all; no download by default — arXiv API is part of the Priority-4 Web tier, see Source Table above):

Policy D2 tracking discipline (orchestrator-managed): the executor (you, the LLM) maintains an in-context list of contributing sources. For helper-backed bash sources (arxiv, semantic-scholar, deepxiv, exa, openalex), a source contributes iff its bash block ran its helper successfully (helper resolved AND invocation exited 0; note: the helper exiting 0 with an empty result list still counts as "ran" — downstream relevance ranking is what decides whether the user actually sees content). For non-helper sources (zotero / obsidian / local PDF / WebSearch / Gemini), the contribution rule is stated in the Step-1 finalization block below — these are tracked separately because they don't emit D2 contribution: log lines from bash. Sources that were not requested via — sources: do not count. At the end of Step 1 (before "Opti