Skillget

research-papers-plugin

skill
Security Audit
Warn
Health Warn
  • No license — Repository has no license file
  • Description — Repository has a description
  • Active repo — Last push 0 days ago
  • Low visibility — Only 7 GitHub stars
Code Pass
  • Code scan — Scanned 12 files during light audit, no dangerous patterns found
Permissions Pass
  • Permissions — No dangerous permissions requested
Purpose
This tool is a plugin that helps you manage, download, and annotate collections of research papers. It integrates with AI coding assistants to automate reading, extracting claims, and cross-referencing academic literature.

Security Assessment
The overall risk is Low. The automated code scan reviewed 12 files and found no dangerous patterns or hardcoded secrets, and the tool does not request any dangerous system permissions. However, there are inherent network considerations: the `paper-retriever` skill is designed to download PDFs from external sources like arXiv, DOI, ACL Anthology, or Sci-Hub. While this is its intended function, users should be aware that it makes outbound network requests and executes file-writing operations on the local disk. It does not appear to access unrelated sensitive data.

Quality Assessment
The project is actively maintained, with its most recent code push happening today. It features a clear, well-documented description and an extensive README detailing its scripts and capabilities. On the downside, the repository lacks a formal open-source license. This means that technically, default copyright laws apply, and the author retains all exclusive rights, which could pose an issue if you plan to heavily modify or redistribute the code. Additionally, with only 7 GitHub stars, the tool has low community visibility and hasn't yet been broadly vetted by a large user base.

Verdict
Use with caution — the code itself appears safe, but the absence of a license and low community adoption mean you should review it internally before integrating it into commercial workflows.
SUMMARY

Research paper collection management plugin for Claude Code, Codex CLI, and Gemini CLI

README.md

research-papers

A plugin for managing annotated research paper collections. Works with Claude Code, Codex CLI, and Gemini CLI.

This repo supports two distribution models:

  • Claude Code marketplace repo via .claude-plugin/marketplace.json
  • Script-based skill installer for Codex CLI and Gemini CLI via scripts/install_skills.py

What it does

This plugin provides skills for retrieving, reading, and annotating scientific papers into a structured, cross-referenced collection. Each paper gets:

  • notes.md — Implementation-focused extraction (equations, parameters, algorithms)
  • description.md — Three-sentence summary
  • abstract.md — Verbatim abstract + interpretation
  • citations.md — Full reference list + key citations for follow-up
  • papers/index.md — Auto-generated list of paper directories in the collection

Skills

Skill Description
paper-retriever Download a paper PDF from arxiv, DOI, ACL Anthology, or sci-hub
paper-reader Read a paper and extract structured notes (handles small/medium/large papers)
paper-process Combined retrieve + read in one step
lint-paper Audit paper directories for completeness and format compliance
reconcile Cross-reference a paper against the collection bidirectionally
tag-papers Add tags to untagged papers using their existing notes
research Web research on a topic, structured findings report
extract-claims Extract/enrich propositional claims from a paper into claims.yaml
make-skill Create new skills from prompt files

Scripts

Repository-level installer utilities live in scripts/. Paper-collection helper scripts live in plugins/research-papers/scripts/.

Script Description
lint_skill_frontmatter.py Parse every SKILL.md frontmatter block and fail on invalid YAML
generate-paper-index.py Rebuild papers/index.md and papers/tagged/ symlinks
cross-reference-papers.py Find cross-references between papers in the collection
migrate-format.py Convert legacy Tags: lines → YAML frontmatter, bold refs → wikilinks
generate_claims.py Parse notes.md and generate claims.yaml for a single paper
batch_generate_claims.py Generate claims.yaml for all papers in a directory
bootstrap_concepts.py Deduplicate and group concept names from claims files

Claims Extraction Pipeline

The claims pipeline extracts machine-readable propositional claims from paper notes. The typical workflow:

  1. generate_claims.py — Parses notes.md (parameter tables, equations, key findings) and produces a draft claims.yaml marked with stage: draft. Fast, deterministic, no LLM needed.
  2. extract-claims skill — LLM-powered enrichment of the draft claims (adds context, fixes types, fills gaps). Can also create claims from scratch if no draft exists.
  3. batch_generate_claims.py — Runs step 1 across an entire papers directory. Use --skip-existing to avoid re-processing.
  4. bootstrap_concepts.py — Collects concept names from all claims files, deduplicates similar names, and outputs a unified concepts list.
# Single paper: generate draft, then enrich with LLM
uv run plugins/research-papers/scripts/generate_claims.py papers/Author_2024_Title
$extract-claims papers/Author_2024_Title

# Batch: generate drafts for all papers missing claims.yaml
uv run plugins/research-papers/scripts/batch_generate_claims.py papers/ --skip-existing

# After batch: deduplicate concepts across all claims
uv run plugins/research-papers/scripts/bootstrap_concepts.py papers/ --output concepts.yaml

Installation

Claude Code marketplace

Use the repo itself as a Claude Code marketplace source. The marketplace manifest lives at .claude-plugin/marketplace.json and currently exposes the plugin ID research-papers@research-papers-marketplace.

git clone https://github.com/ctoth/research-papers-plugin
cd research-papers-plugin
claude plugin marketplace add . --scope user
claude plugin install research-papers@research-papers-marketplace --scope user

If your clone already exists somewhere else, replace . with that repo path.

Script-based installer for Codex CLI and Gemini CLI

Use the bundled installer when you want the skills installed into Codex and/or Gemini user skill directories:

uv run scripts/install_skills.py doctor
uv run scripts/install_skills.py install --platform codex --platform gemini

What the installer does:

  • discovers every skill directory under plugins/*/skills/*
  • installs Codex skills into ~/.agents/skills
  • installs Gemini skills into ~/.gemini/skills
  • prefers whole-directory symlinks and falls back to copying if symlinks are unavailable

Useful variants:

uv run scripts/lint_skill_frontmatter.py
uv run scripts/install_skills.py install
uv run scripts/install_skills.py install --platform codex
uv run scripts/install_skills.py install --platform gemini
uv run scripts/install_skills.py install --platform claude
uv run scripts/install_skills.py uninstall

install --platform claude uses Claude's native claude plugin marketplace add/install flow under the hood. Omitting --platform installs all supported targets.

Project setup

Your project needs this structure:

your-project/
├── papers/
│   ├── index.md     # Paper listing with tags (auto-generated)
│   ├── tagged/       # Symlinks organized by tag (auto-generated)
│   │   ├── acoustics/
│   │   │   └── Fant_1985_LFModel -> ../../Fant_1985_LFModel
│   │   └── voice-quality/
├── reports/          # Research output
└── prompts/          # Prompt templates for large papers

Copy plugins/research-papers/templates/papers-gitignore into your .gitignore to exclude PDFs from git.

Usage

Claude Code

After marketplace install:

/research-papers:paper-process https://arxiv.org/abs/2104.01005
/research-papers:research screen reader accessibility
/research-papers:paper-reader papers/Mack_2021_AccessibilityResearch/paper.pdf

Codex CLI

Run Codex from the project repo that contains your papers/ directory, then invoke the installed skills explicitly:

$paper-process https://arxiv.org/abs/2104.01005
$research screen-reader accessibility
$paper-reader papers/Mack_2021_AccessibilityResearch/paper.pdf
$extract-claims papers/Author_2024_Title

Some skill command examples use scripts/... paths. Those are skill-local paths relative to the installed skill directory, not paths relative to the user's project repo.

Codex can also auto-select these skills from a natural-language prompt, but explicit $skill-name invocation is the most reliable way to verify the install.

Gemini CLI

Run Gemini from the project repo that contains your papers/ directory. Gemini loads the installed skills from ~/.gemini/skills; unlike Codex, it does not use $skill-name command syntax, so invoke the skill by name in your prompt:

Use the paper-process skill on https://arxiv.org/abs/2104.01005
Use the research skill to investigate screen reader accessibility
Use the paper-reader skill on papers/Mack_2021_AccessibilityResearch/paper.pdf

Requirements

  • An agent CLI: Claude Code 1.0.33+, Codex CLI, or Gemini CLI
  • curl for downloading papers
  • ImageMagick (magick) for large paper PDF-to-image conversion
  • Python 3 for cross-reference script
  • Playwright MCP server for paywalled papers (optional, works on all platforms):
    • Claude Code: claude mcp add playwright -- npx @playwright/mcp@latest
    • Codex CLI: add [mcp_servers.playwright] to ~/.codex/config.toml
    • Gemini CLI: add to ~/.gemini/settings.json mcpServers

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