| 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
- Initialize repository structure - Create directory layout and core files
- Configure domain specifics - Customize priorities, tags, and templates
- Set up Claude Code Skills - Create domain-specific search and add workflows
- 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
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**
> **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:
Skills:
Git:
⚠️ 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.
Reference Materials
Quick Reference Navigation
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
- Skill-based automation: Complex workflows encoded as discoverable, executable commands
- Progressive disclosure: Quick reference (CLAUDE.md) → deep dive (reference docs)
- Priority-driven focus: Ensures attention on core research areas
- Local-global separation: Personal insights (local) vs. polished repository (public)
- 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
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
