git:20260307.79c583f to git:20260308.9e94117

54 added, 9 removed. Audit A to A.

---

name: research-repo

- description: "Create and set up automated research repositories for curating academic papers in any domain. Use when user wants to start a new research tracking repository, migrate existing literature collection to AI-assisted workflow, or establish standardized workflows for paper discovery and documentation"

+ 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](references/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:

```bash

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](references/templates/core-files.md) (CLAUDE.md, research-focus.md, classification-guide.md), [git-config.md](references/templates/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](references/setup-wizard.md) for interactive configuration.

Customize these files for your research domain:

|------|---------|-------------------|----------|

| **CLAUDE.md** | Primary instructions for Claude Code | Repository purpose, primary skills, research focus, essential principles | [template](references/templates/core-files.md#claude-md) |

| **research-focus.md** | Research priorities and search strategy | Priority definitions (3 tiers), search strategies, decision trees, quality criteria | [template](references/templates/core-files.md#research-focus-md) |

| **classification-guide.md** | Tagging system and classification standards | Tag categories (3-4), color scheme, selection rules, examples | [template](references/templates/core-files.md#classification-guide-md) |

**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](references/faq.md#priority-and-classification)

### 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](references/setup-wizard.md#phase-55-create-domain-specific-skills) 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**:

```bash

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

```

**Required files**:

- | File | Purpose | Template |

- |------|---------|----------|

- | `SKILL.md` | Main skill definition | [search-items template](references/templates/skills/search-items-skill.md) |

- | `references/queries.md` | Domain-specific search queries (30-50 total) | See template in search-items-skill.md |

+ | File | Purpose | How to create |

+ |------|---------|---------------|

+ | `SKILL.md` | Main skill definition with complete workflow | **READ** the [search-items template](references/templates/skills/search-items-skill.md), **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**:

```bash

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

```

**Required files**:

- | File | Purpose | Template |

- |------|---------|----------|

- | `SKILL.md` | Main skill definition | [add-item template](references/templates/skills/add-item-skill.md) |

- | `references/notes-template.md` | Local notes structure | See template in add-item-skill.md |

+ | File | Purpose | How to create |

+ |------|---------|---------------|

+ | `SKILL.md` | Main skill definition with complete workflow | **READ** the [add-item template](references/templates/skills/add-item-skill.md), **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](references/faq.md#skills-and-workflow)

### Step 4: Initialize README Files

| File | Purpose | Template |

|------|---------|----------|

| **README.md** | Main repository content (English) | See [readme-entry.md](references/templates/readme-entry.md) for entry format |

| **README_zh.md** | Chinese translation (optional) | Mirror English structure |

**README.md structure**:

```markdown

# [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**:

```bash

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](references/faq.md#git-workflow)

### 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.

---

## Reference Materials

### Quick Reference Navigation

| Resource | Purpose | Trigger Condition |

|----------|---------|-------------------|

| [setup-wizard.md](references/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](references/faq.md) | Common questions and troubleshooting | **User encounters issues** or asks about best practices |

| [templates/core-files.md](references/templates/core-files.md) | CLAUDE.md, research-focus.md, classification-guide.md | **Step 2** - Creating core configuration files |

| [templates/git-config.md](references/templates/git-config.md) | .gitignore, LICENSE | **Step 2** - Git setup |

| [templates/skills/search-items-skill.md](references/templates/skills/search-items-skill.md) | search-[items] skill template | **Step 3A** - Creating search skill |

| [templates/skills/add-item-skill.md](references/templates/skills/add-item-skill.md) | add-[item] skill template | **Step 3B** - Creating add skill |

| [templates/readme-entry.md](references/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](references/setup-wizard.md#example-domains):

- AI-for-Climate-Change

- LLM-for-Education

- Quantum-Computing-Papers

---

## Need Help?

See [faq.md](references/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