# Claude Code Plugin Setup - Summary

## ✅ What Was Created

Your `claude-scientific-writer` repository is now fully configured as a Claude Code plugin! Here's what was set up:

### 1. Plugin Infrastructure

- **`.claude-plugin/plugin.json`** - Plugin metadata and configuration
- **`commands/scientific-writer-init.md`** - `/scientific-writer:init` command implementation
- **`templates/CLAUDE.scientific-writer.md`** - CLAUDE.md template for project initialization
- **`test-marketplace-example.json`** - Example marketplace configuration for testing

### 2. Skills (19 Total)

All skills from `.claude/skills/` have been copied to the top-level `skills/` directory with proper YAML frontmatter:

1. **citation-management** - BibTeX, DOI lookup, Google Scholar/PubMed search
2. **clinical-decision-support** - Cohort analysis, biomarker reports, treatment recommendations
3. **clinical-reports** - Case reports, trial documentation, HIPAA compliance
4. **document-skills** - DOCX, PDF, PPTX, XLSX manipulation
5. **hypothesis-generation** - Research hypothesis development
6. **latex-posters** - Conference poster generation
7. **literature-review** - Systematic reviews, PRISMA workflows
8. **markitdown** - Document format conversion
9. **paper-2-web** - Convert papers to web format
10. **peer-review** - Manuscript evaluation, ScholarEval framework
11. **research-grants** - NSF, NIH, DOE, DARPA proposals
12. **research-lookup** - Real-time literature search via Perplexity
13. **scholar-evaluation** - Academic quality assessment
14. **scientific-critical-thinking** - Research methodology critique
15. **scientific-schematics** - CONSORT diagrams, circuit diagrams
16. **scientific-slides** - Conference presentations, Beamer slides
17. **scientific-writing** - IMRaD structure, journal formatting
18. **treatment-plans** - Clinical treatment documentation
19. **venue-templates** - Journal/conference templates

### 3. Documentation

- **README.md** - Updated with:
  - Claude Code plugin installation instructions
  - Plugin testing guide for local development
  - Troubleshooting section
  
## 📁 Final Structure

```
claude-scientific-writer/
├── .claude/                    # Local development (existing)
├── .claude-plugin/
│   └── plugin.json            # ✨ NEW - Plugin metadata
├── commands/
│   └── scientific-writer-init.md  # ✨ NEW - Init command
├── skills/                    # ✨ NEW - All 19 skills
│   ├── citation-management/
│   ├── clinical-decision-support/
│   ├── clinical-reports/
│   ├── document-skills/
│   ├── hypothesis-generation/
│   ├── latex-posters/
│   ├── literature-review/
│   ├── markitdown/
│   ├── paper-2-web/
│   ├── peer-review/
│   ├── research-grants/
│   ├── research-lookup/
│   ├── scholar-evaluation/
│   ├── scientific-critical-thinking/
│   ├── scientific-schematics/
│   ├── scientific-slides/
│   ├── scientific-writing/
│   ├── treatment-plans/
│   └── venue-templates/
├── templates/
│   └── CLAUDE.scientific-writer.md  # ✨ NEW - CLAUDE.md template
├── test-marketplace-example.json    # ✨ NEW - Testing helper
├── PLUGIN_SETUP_SUMMARY.md          # ✨ NEW - This file
└── ... (existing Python package files)
```

## 🚀 Next Steps

### For End Users

Users can now install your plugin in Claude Code (Cursor):

```bash
# In Claude Code:
/plugin marketplace add https://github.com/K-Dense-AI/claude-scientific-writer
/plugin install claude-scientific-writer

# In any project:
/scientific-writer:init
```

### For Local Testing (Developers)

1. **Create test marketplace** (in parent directory):
   ```bash
   cd ..
   mkdir -p test-marketplace/.claude-plugin
   # Copy test-marketplace-example.json to test-marketplace/.claude-plugin/marketplace.json
   # Update the "source" path to point to your local repo
   ```

2. **Install in Claude Code**:
   ```bash
   /plugin marketplace add ./test-marketplace
   /plugin install claude-scientific-writer@test-marketplace
   # Restart when prompted
   ```

3. **Test**:
   ```bash
   # In any project:
   /scientific-writer:init
   # Should create CLAUDE.md and enable all skills
   ```

### For Publishing

When ready to publish to a public marketplace (like claude-market/marketplace):

1. Push changes to GitHub
2. Create a release/tag
3. Submit to the marketplace repository following their guidelines

## ✨ Key Features

### The `/scientific-writer:init` Command

When users run this command, it:
- Checks for existing CLAUDE.md (offers backup/merge/replace)
- Creates CLAUDE.md with full scientific writing instructions
- Makes all 19 skills available
- Provides onboarding summary with examples

### Skills Are Automatically Available

Once the plugin is installed, users can:
- Reference skills: `@research-lookup find papers on CRISPR`
- Ask: "What skills are available?"
- Use naturally: "Create a Nature paper on quantum computing" (automatically uses relevant skills)

### Project-Specific Configuration

Each project gets its own CLAUDE.md that can be customized while still having access to all plugin skills.

## 🔧 Maintenance

### Updating Skills

When you update skills in `.claude/skills/`:
1. Copy changes to `skills/`: `cp -R .claude/skills/* skills/`
2. Verify YAML frontmatter is intact
3. Test locally before pushing

### Updating the Template

When you update `CLAUDE.md`:
1. Update `templates/CLAUDE.scientific-writer.md`
2. Keep the HTML comment header
3. Test the init command

## 📚 References

- [Claude Code Plugin Docs](https://docs.claude.ai/docs/agent-plugins)
- [Agent Skills Format](https://docs.claude.ai/docs/agent-skills)
- [GitHub Repository](https://github.com/K-Dense-AI/claude-scientific-writer)

## ✅ Verification Checklist

- [x] `.claude-plugin/plugin.json` exists with valid JSON
- [x] All 19 skills copied to `skills/` directory
- [x] Each `SKILL.md` has valid YAML frontmatter (name, description, allowed-tools)
- [x] `commands/scientific-writer-init.md` created with proper format
- [x] `templates/CLAUDE.scientific-writer.md` created from CLAUDE.md
- [x] README.md updated with plugin usage and testing instructions
- [x] Test marketplace example provided

## 🎉 Status: Complete!

Your Claude Code plugin is ready for use and distribution!

