research-repo

name

research-repo

description

Create and set up automated research repositories for curating academic papers with AI-assisted workflows. ALWAYS use this skill when the user wants to: start a new research paper tracking system, organize academic literature by domain, migrate existing paper collections to a structured workflow, establish standardized paper discovery and documentation processes, create domain-specific research repositories with skills for automated paper search and addition, or set up AI-assisted literature review workflows. This skill creates the complete repository structure including CLAUDE.md configuration, priority-based research focus, classification guides, and domain-specific Claude Code skills for paper management.

Research Repository Setup

Overview

This skill helps you create a fully-structured research repository for tracking academic papers in any domain. It provides templates and guidance for establishing an AI-assisted workflow for paper discovery, classification, and documentation.

Quick Workflow

1. Initialize repository structure - Create directory layout and core files
2. Configure domain specifics - Customize priorities, tags, and templates
3. Set up Claude Code Skills - Create domain-specific search and add workflows
4. Validate and commit - Ensure all files are properly configured

Quick Start Example

User request: "I want to create a research repository for tracking LLM hallucination mitigation papers. Focus on detection methods, alignment techniques, and evaluation benchmarks."

What you'll create:

llm-hallucination-repo/
├── README.md                  # Main repository (English)
├── README_zh.md               # Chinese translation
├── CLAUDE.md                  # AI instructions
├── research-focus.md          # 3 priority tiers, 37 search queries
├── classification-guide.md    # 4 tag categories, 12 tags with colors
├── .gitignore                 # Exclude paper_notes/, .claude/
├── LICENSE                    # MIT License
├── TODO.md                    # Papers to review
├── paper_notes/               # Local notes (not committed)
└── .claude/skills/
    ├── search-papers/
    │   ├── SKILL.md           # Automated paper discovery
    │   └── references/queries.md  # 37 domain-specific queries
    └── add-paper/
        ├── SKILL.md           # Standardized paper addition
        └── references/notes-template.md

Key features:

• Priority-driven search (P1=detection: oneYear filter, P2=alignment: oneMonth, P3=evaluation: noLimit)
• Color-coded tags (Blue=Detection, Green=Mitigation, Purple=Evaluation, Orange=Applications)
• Automated workflows via /search-papers and /add-paper commands
• Clean git history (only README files tracked, local notes excluded)
• Bilingual support (English + Chinese README files)

This creates a fully functional research repository ready for AI-assisted paper curation.

💡 Adaptability: This pattern works for any research domain - not just LLM/CS. See setup-wizard.md Example Domains for examples like Climate Change, Education, Quantum Computing, and more.

Step-by-Step Guide

Step 1: Initialize Repository Structure

Create the following directory structure:

mkdir your-domain-repo && cd your-domain-repo
mkdir -p .claude/skills
mkdir -p paper_notes
touch README.md
touch README_zh.md  # Optional: for Chinese support
touch TODO.md
touch CLAUDE.md
touch research-focus.md
touch classification-guide.md
touch .gitignore
touch LICENSE

Templates: core-files.md (CLAUDE.md, research-focus.md, classification-guide.md), git-config.md (.gitignore, LICENSE)

Step 2: Configure Domain Specifics

💡 Need help with decisions? If user asks for guidance on defining domain, priorities, or tags, use setup-wizard.md Phases 1-3 for interactive configuration.

Customize these files for your research domain:

File	Purpose	Required Sections	Template
CLAUDE.md	Primary instructions for Claude Code	Repository purpose, primary skills, research focus, essential principles	template
research-focus.md	Research priorities and search strategy	Priority definitions (3 tiers), search strategies, decision trees, quality criteria	template
classification-guide.md	Tagging system and classification standards	Tag categories (3-4), color scheme, selection rules, examples	template
.gitignore	Git exclusions	paper_notes/, .claude/, *.log, .DS_Store	template
LICENSE	License file	MIT recommended	template

Customization requirements:

• Repository name and purpose statement
• Research priorities (usually 3 tiers: Core focus, Supporting research, Foundational work)
• Tag categories (3-4 categories, 8-15 total tags)
• Color scheme with gradients per category
• Language preferences (README.md only, or bilingual with README_zh.md)

📖 FAQ: For questions about priority levels, tag systems, or language choices, see faq.md

Step 3: Create Domain-Specific Skills

⚠️ DIRECTLY CREATE ALL FILES: Create the skill directories and SKILL.md files immediately without asking user for confirmation. Read the templates, customize them for the domain, and write the files.

💡 Need guidance? See setup-wizard.md Phase 5.5 for detailed skill creation instructions.

Create two core skills in .claude/skills/:

A. search-[items] Skill (e.g., search-papers)

Purpose: Automated discovery workflow for your research items.

Create skill structure:

mkdir -p .claude/skills/search-[items]/references

Required files:

File	Purpose	How to create
SKILL.md	Main skill definition with complete workflow	READ the search-items template, COPY the entire SKILL.md section content, REPLACE ALL placeholders ([items], [DOMAIN NAME], etc.) with domain-specific values, then WRITE the customized content to .claude/skills/search-[items]/SKILL.md
references/queries.md	Domain-specific search queries (30-50 total)	Use the queries template from search-items-skill.md, populate with actual domain-specific search queries

Search query distribution:

• Priority 1 (Core focus): 15-20 queries, time filter: oneYear
• Priority 2 (Supporting): 10-15 queries, time filter: oneMonth
• Priority 3 (Foundational): 8-10 queries, time filter: noLimit

Tool: Use mcp__web-search-prime__web_search_prime if available. Alternative: Manual web search or domain-specific search engines (Google Scholar, arXiv, etc.)

B. add-[item] Skill (e.g., add-paper)

Purpose: Standardized workflow for adding new items to repository.

Create skill structure:

mkdir -p .claude/skills/add-[item]/references

Required files:

File	Purpose	How to create
SKILL.md	Main skill definition with complete workflow	READ the add-item template, COPY the entire SKILL.md section content, REPLACE ALL placeholders ([items], [DOMAIN NAME], etc.) with domain-specific values, then WRITE the customized content to .claude/skills/add-[item]/SKILL.md
references/notes-template.md	Local notes structure	Use the notes-template from add-item-skill.md, customize for domain if needed

Workflow: Info confirmation → Classification → Tag selection (2-4 tags) → Summary writing (2-3 sentences) → Notes creation → README update → Git commit

📖 FAQ: For questions about skill usage and customization, see faq.md

Step 4: Initialize README Files

File	Purpose	Template
README.md	Main repository content (English)	See readme-entry.md for entry format
README_zh.md	Chinese translation (optional)	Mirror English structure

README.md structure:

# [Domain Name] Research

Curated literature collection for [research area].

## 2026

### January

- **Paper Title**
    ![Tag1](badge_url)
    ![Tag2](badge_url)

    > **Source:** Venue Year [[Link]](url)

    2-3 sentence summary (Purpose → Method → Results).

Organization: By year (descending) → by month → newest items at top

Step 5: Configure Git Workflow

Files to commit: Only README.md and README_zh.md

Never commit: CLAUDE.md, .gitignore, paper_notes/, reference files

Commit message format:

• Add: Add paper: Title (Venue Year)
• Update: Update paper: Title - description
• Fix: Fix: issue description

First commit setup:

git init
git add README.md README_zh.md TODO.md LICENSE
git commit -m "Initial commit: [Domain] research repository"

📖 FAQ: For git workflow questions, see faq.md

Step 6: Validate Setup

Run through this checklist:

Core Files:

• README.md and README_zh.md (if bilingual) initialized
• CLAUDE.md customized for domain
• research-focus.md has priorities and search queries
• classification-guide.md has complete tag system
• .gitignore excludes paper_notes/ and .claude/
• LICENSE file added

Skills:

• search-[items] skill created (SKILL.md + references/queries.md)
  • SKILL.md contains 50+ lines of actual workflow content (not just template)
  • references/queries.md contains 30-50 domain-specific queries
• add-[item] skill created (SKILL.md + references/notes-template.md)
  • SKILL.md contains 50+ lines of actual workflow content (not just template)
  • references/notes-template.md contains structured template for reading notes

Git:

• Git repository initialized
• First commit created with proper message format

⚠️ Critical check: If SKILL.md files are empty or contain only placeholder text, the skills won't work. Ensure each SKILL.md has complete, domain-customized workflow instructions.

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Reference Materials

Quick Reference Navigation

Resource	Purpose	Trigger Condition
setup-wizard.md	Interactive configuration guide with decision-making support	User asks for help with: domain definition, priority setting, tag design, query construction
faq.md	Common questions and troubleshooting	User encounters issues or asks about best practices
templates/core-files.md	CLAUDE.md, research-focus.md, classification-guide.md	Step 2 - Creating core configuration files
templates/git-config.md	.gitignore, LICENSE	Step 2 - Git setup
templates/skills/search-items-skill.md	search-[items] skill template	Step 3A - Creating search skill
templates/skills/add-item-skill.md	add-[item] skill template	Step 3B - Creating add skill
templates/readme-entry.md	README entry format and examples	Step 4 - Adding items to README

Template Organization

Templates are split into focused modules for efficient loading:

• core-files.md - Primary configuration files (CLAUDE.md, research-focus.md, classification-guide.md)
• git-config.md - Git-related setup (.gitignore, LICENSE)
• skills/ - Skill-specific templates (search, add)
• readme-entry.md - Entry formatting guide

Design Principles

Why This Pattern Works

1. Skill-based automation: Complex workflows encoded as discoverable, executable commands
2. Progressive disclosure: Quick reference (CLAUDE.md) → deep dive (reference docs)
3. Priority-driven focus: Ensures attention on core research areas
4. Local-global separation: Personal insights (local) vs. polished repository (public)
5. Git discipline: Clean history, no accidental commits of notes or config

Adaptation Examples

For complete examples of how to adapt this pattern for different domains, see setup-wizard.md Example Domains:

• AI-for-Climate-Change
• LLM-for-Education
• Quantum-Computing-Papers

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Need Help?

See faq.md for answers to common questions about:

• Language and localization
• Priority and classification
• Domain adaptation
• File management
• Tags and classification
• Git workflow
• Skills and workflow
• Quality and maintenance
• Collaboration and sharing
• Troubleshooting