read-paper

name

read-paper

description

How to read and work with academic paper folders exported by ZoFiles. Each paper folder (named like `{arxivId} - {title}`) contains structured files: paper.md (full text), paper.bib (citation), kimi.md (AI review), arxiv.id, notes/, and paper.pdf. Use this skill whenever the user asks you to read a paper, summarize a paper, cite a paper, review a paper, compare papers, or work with any folder that contains paper.md/paper.bib/kimi.md files — even if they don't mention "ZoFiles" explicitly. Also use when the user asks to update/refresh the paper library directory structure (e.g. "Update paper library directory structure", "refresh paper library").

Reading Paper Folders

Paper folders are exported by ZoFiles from Zotero. Each folder is named {arxivId} - {title} and contains structured files about one academic paper.

Paper Library Location

The paper library is at:

<FILL_IN: ask the user for their ZoFiles export root path, then update this file>

First-use setup: If the path above says <FILL_IN...> or doesn't exist, ask the user: "What's the path to your ZoFiles paper library?" Then:

1. Update the path above
2. Run scan-library.sh to populate the directory snapshot (see Updating the Directory Snapshot)

Directory Structure

The library mirrors Zotero's collection hierarchy. Collections become directories, sub-collections become subdirectories, and paper folders sit at the leaves.

Key patterns:

• Allin/ directories appear when a collection has subcollections — contains all papers from that collection and every descendant (flat view of the entire subtree).
• Paper folders are named {arxivId} - {title} (e.g. 2512.18832 - From Word to World...).
• Find by arXiv ID: glob **/2512.18832* from the library root.
• Browse a topic: list the corresponding collection directory.
• See all papers: glob **/paper.md or **/arxiv.id recursively.

Current Library Snapshot

<FILL_IN: run the scan script below to populate this snapshot>

Use this snapshot to quickly orient yourself when the user asks about topics, collections, or paper counts — no need to scan the filesystem each time.

Updating the Directory Snapshot

When the user asks to update the directory structure (e.g. "更新目录", "update directory", "refresh library"):

bash .claude/skills/read-paper/scripts/scan-library.sh "<library_root>"

Then replace the content between <!-- AUTO-GENERATED --> and <!-- END AUTO-GENERATED --> markers in this file with the new output (wrapped in a ```code block), and update the<!-- Last updated: ... --> date.

Files in a Paper Folder

File	What it is	When to read
paper.md	Full-text Markdown of the paper	Primary source. Read this for any paper-related task.
paper.bib	BibTeX citation entry	When citing. Always copy verbatim — never generate BibTeX yourself.
kimi.md	AI-generated review in Chinese (structured Q&A)	Quick overview without reading the full paper. Verify claims against paper.md.
arxiv.id	Plain text arXiv ID (e.g. 2505.17746)	When you need the identifier or arXiv URL.
notes/	User's personal notes (Markdown files)	When the user asks about their notes or annotations.
paper.pdf	Original PDF (or symlink)	Only if specifically asked — prefer paper.md.

Not all files may be present. If a file is missing (e.g. no kimi.md or paper.md), skip it gracefully and work with what's available. Never tell the user a file "should" exist — just use alternative sources. For example, if paper.md is missing, fall back to paper.pdf; if kimi.md is missing, just read paper.md directly.

How to Read paper.md

paper.md starts with YAML frontmatter, then a table of contents, then the full text:

---
title: "Paper Title"
authors: ["Author 1", "Author 2"]
url: "https://arxiv.org/abs/XXXX.XXXXX"
sections: 27
estimated_tokens: "12.9k"
---
## Contents
- 1 Introduction
- 2 Related Works
  - 2.1 ...
...

Reading strategy:

1. Always start with frontmatter + ToC — gives you structure, size, and lets you plan what to read
2. Read selectively — use the ToC to jump to relevant sections; don't read the whole paper unless asked
3. Quick overview → Introduction + Conclusion
4. Methodology → Methods/Approach section
5. Results → Experiments/Results/Evaluation sections

For large papers (>15k tokens), use offset/limit on the Read tool. Ask yourself which sections actually answer the user's question.

Citations

Always read paper.bib and copy the BibTeX entry exactly as-is. Never modify, reformat, or regenerate BibTeX — hand-generated citations often contain errors. The exported BibTeX is sourced from arXiv and is authoritative.

Common Tasks

User request	What to do
"Summarize this paper"	Read paper.md: Introduction + Conclusion. Optionally skim kimi.md for a second perspective.
"What's the main contribution?"	Read the Introduction section of paper.md.
"Give me the BibTeX"	Read paper.bib, copy verbatim.
"Compare these papers"	Read paper.md from each folder (Introduction + Methods + Results).
"What did I note about this?"	Read files in the notes/ directory.
"What's the arXiv ID?"	Read arxiv.id.
"更新目录" / "Update directory"	Run scan-library.sh, update the snapshot in this file.