# Complete Documentation Index

**Scientific Writer v2.7.0** - Comprehensive documentation navigation guide.

---

## 📚 Documentation Structure

### Core Documentation (Start Here)

| Document | Purpose | Audience | Last Updated |
|----------|---------|----------|--------------|
| [README.md](../README.md) | Main entry point, quick start, features overview | Everyone | v2.7.0 |
| [docs/README.md](README.md) | Documentation hub with navigation guide | Everyone | v2.7.0 |
| [CHANGELOG.md](../CHANGELOG.md) | Version history and release notes | Everyone | v2.7.0 |

### User Guides

| Document | Content | When to Read |
|----------|---------|--------------|
| [FEATURES.md](FEATURES.md) | Complete feature guide (document generation, AI capabilities, file integration) | To understand what's possible |
| [SKILLS.md](SKILLS.md) | All 19+ skills with examples | To learn available capabilities |
| [API.md](API.md) | Programmatic API reference with code examples | When using Python API |
| [TROUBLESHOOTING.md](TROUBLESHOOTING.md) | Common issues and solutions | When you encounter problems |

### Developer Resources

| Document | Content | Audience |
|----------|---------|----------|
| [DEVELOPMENT.md](DEVELOPMENT.md) | Architecture, plugin development, contributing | Contributors, maintainers |
| [RELEASING.md](RELEASING.md) | Version management, PyPI publishing | Maintainers |
| [example_api_usage.py](../example_api_usage.py) | Working Python examples | API users |
| [TESTING_INSTRUCTIONS.md](../TESTING_INSTRUCTIONS.md) | Plugin testing guide | Plugin developers |

### System Documentation

| Document | Content | Audience |
|----------|---------|----------|
| [CLAUDE.md](../CLAUDE.md) | System instructions for the AI agent | Advanced users, developers |

---

## 🎯 Quick Navigation by Use Case

### I Want to Install and Use Scientific Writer

**As a Claude Code Plugin (Recommended):**
1. Start: [Plugin Installation Guide](../README.md#-use-as-a-claude-code-plugin-recommended)
2. Reference: [Skills Overview](SKILLS.md)
3. Troubleshoot: [Plugin Issues](TROUBLESHOOTING.md)

**As a CLI Tool:**
1. Start: [Installation](../README.md#installation-options) → [CLI Usage](../README.md#use-the-cli)
2. Reference: [Common Commands](../README.md#common-commands)
3. Troubleshoot: [CLI Issues](TROUBLESHOOTING.md)

**As a Python API:**
1. Start: [API Quick Start](../README.md#use-the-python-api)
2. Reference: [API Documentation](API.md)
3. Examples: [example_api_usage.py](../example_api_usage.py)

### I Want to Generate Specific Documents

| Document Type | Getting Started | Detailed Guide | Examples |
|--------------|----------------|----------------|----------|
| **Research Papers** | [Quick Start](../README.md#quick-start) | [Features: Papers](FEATURES.md#scientific-papers) | [README Examples](../README.md#common-commands) |
| **Grant Proposals** | [Grant Commands](../README.md#common-commands) | [Skills: Grants](SKILLS.md#5-research-grants) | [Features: Grants](FEATURES.md#grant-proposals) |
| **Research Posters** | [Poster Commands](../README.md#common-commands) | [Skills: Posters](SKILLS.md#8-latex-research-posters) | [Features: Posters](FEATURES.md#research-posters) |
| **Clinical Reports** | [Clinical Commands](../README.md#common-commands) | [Skills: Clinical](SKILLS.md#6-clinical-reports) | [Features: Clinical](FEATURES.md#document-generation) |
| **Literature Reviews** | [Review Commands](../README.md#common-commands) | [Skills: Literature](SKILLS.md#2-literature-review) | [Features: Reviews](FEATURES.md#literature-reviews) |
| **Presentations** | [Slides Examples](../README.md#common-commands) | [Skills: Slides](SKILLS.md#9-scientific-slides-and-presentations) | [CLAUDE.md: Presentations](../CLAUDE.md) |

### I Want to Use Specific Features

| Feature | Documentation | Skills Involved |
|---------|---------------|-----------------|
| **Research Lookup** | [Features: Research Lookup](FEATURES.md#real-time-research-lookup) | [research-lookup](SKILLS.md#research-lookup) |
| **Peer Review** | [Features: Peer Review](FEATURES.md#peer-review-with-scholareval) | [peer-review](SKILLS.md#3-peer-review), [scholar-evaluation](SKILLS.md#4-scholar-evaluation) |
| **Citation Management** | [Skills: Citations](SKILLS.md#citation-management) | [citation-management](SKILLS.md) |
| **Document Conversion** | [Features: Conversion](FEATURES.md#document-conversion) | [markitdown](SKILLS.md#12-markitdown---universal-file-to-markdown-converter) |
| **Scientific Schematics** | [Features: Schematics](FEATURES.md#scientific-schematics) | [scientific-schematics](SKILLS.md#10-scientific-schematics-and-diagrams) |

### I Want to Develop or Contribute

**Plugin Development:**
1. [Plugin Structure](DEVELOPMENT.md#plugin-structure)
2. [Local Testing](DEVELOPMENT.md#testing-plugin-locally)
3. [Testing Guide](../TESTING_INSTRUCTIONS.md)

**Python Package Development:**
1. [Architecture](DEVELOPMENT.md#architecture-overview)
2. [Setup](DEVELOPMENT.md#local-development)
3. [Contributing](DEVELOPMENT.md#contributing)

**Publishing:**
1. [Version Management](RELEASING.md#bump-the-version-semver)
2. [Publishing to PyPI](RELEASING.md#publish-to-pypi)
3. [Verification](RELEASING.md#verify)

---

## 🔗 External Resources

- **GitHub Repository**: https://github.com/K-Dense-AI/claude-scientific-writer
- **PyPI Package**: https://pypi.org/project/scientific-writer/
- **Community Slack**: [Join K-Dense Community](https://join.slack.com/t/k-densecommunity/shared_invite/zt-3iajtyls1-EwmkwIZk0g_o74311Tkf5g)
- **Issue Tracker**: https://github.com/K-Dense-AI/claude-scientific-writer/issues

---

## 📊 Documentation Health Check

### Completeness

- ✅ Installation guides (Plugin, CLI, API)
- ✅ Usage examples (all document types)
- ✅ API reference (complete with examples)
- ✅ Skills documentation (19+ skills)
- ✅ Troubleshooting guide
- ✅ Development guide
- ✅ Release process
- ✅ Change log

### Accuracy

- ✅ Version numbers updated (v2.7.0)
- ✅ Links verified
- ✅ Examples tested
- ✅ Prerequisites current

### Coverage

- ✅ All three usage modes documented (Plugin, CLI, API)
- ✅ All major features covered
- ✅ All skills documented
- ✅ Common issues addressed

---

## 🎓 Learning Path

### Beginner Path (First-Time Users)

1. Read: [Main README](../README.md) (5 min)
2. Install: Follow [Plugin Installation](../README.md#-use-as-a-claude-code-plugin-recommended) (2 min)
3. Try: Create your first document (10 min)
4. Explore: Browse [Skills Overview](SKILLS.md) (10 min)

### Intermediate Path (Regular Users)

1. Master: [Common Commands](../README.md#common-commands)
2. Learn: [Research Lookup](FEATURES.md#real-time-research-lookup)
3. Use: [Peer Review](FEATURES.md#peer-review-with-scholareval)
4. Optimize: [File Integration](FEATURES.md#data--file-integration)

### Advanced Path (Power Users)

1. API: Read [API Reference](API.md)
2. Customize: Understand [System Instructions](../CLAUDE.md)
3. Extend: Learn [Plugin Development](DEVELOPMENT.md)
4. Contribute: Follow [Contributing Guide](DEVELOPMENT.md#contributing)

---

## 📝 Documentation Conventions

### File Organization

```
claude-scientific-writer/
├── README.md                    # Main entry point
├── CHANGELOG.md                 # Version history
├── CLAUDE.md                    # System instructions
├── TESTING_INSTRUCTIONS.md      # Plugin testing
├── example_api_usage.py         # API examples
├── docs/
│   ├── README.md                # Documentation hub
│   ├── DOCUMENTATION_INDEX.md   # This file
│   ├── API.md                   # API reference
│   ├── FEATURES.md              # Feature guide
│   ├── SKILLS.md                # Skills reference
│   ├── TROUBLESHOOTING.md       # Problem solving
│   ├── DEVELOPMENT.md           # Developer guide
│   ├── RELEASING.md             # Release process
│   └── examples/                # Example outputs
└── skills/                      # 19+ skill directories
```

### Link Format

- **Internal links**: Relative paths (e.g., `[text](../README.md)`)
- **External links**: Full URLs (e.g., `https://github.com/...`)
- **Anchors**: Lowercase with hyphens (e.g., `#quick-start`)

### Version References

- Always specify version when referencing features (e.g., "v2.7.0")
- Use "Latest" for current version, "Previous" for older versions
- Update version numbers during releases

---

## 🔄 Maintenance Schedule

### Regular Updates (Each Release)

- [ ] Update version numbers in all docs
- [ ] Update CHANGELOG.md with new features
- [ ] Review and update README.md examples
- [ ] Verify all links still work
- [ ] Update "Last Updated" dates

### Quarterly Reviews

- [ ] Check for outdated information
- [ ] Add new examples based on user feedback
- [ ] Review and update troubleshooting guide
- [ ] Update screenshots if UI changed
- [ ] Review documentation completeness

### Annual Updates

- [ ] Major documentation restructuring if needed
- [ ] Update learning paths based on usage patterns
- [ ] Comprehensive link checking
- [ ] Update external resource links
- [ ] Review and update conventions

---

## 💬 Feedback

Found an issue with the documentation? Please:

1. **Check**: [Troubleshooting Guide](TROUBLESHOOTING.md)
2. **Search**: [GitHub Issues](https://github.com/K-Dense-AI/claude-scientific-writer/issues)
3. **Report**: Create a new issue with the "documentation" label
4. **Discuss**: Join our [Slack Community](https://join.slack.com/t/k-densecommunity/shared_invite/zt-3iajtyls1-EwmkwIZk0g_o74311Tkf5g)

---

**Last Updated**: January 22, 2025 (v2.7.0)

**Documentation Status**: ✅ Complete and Current

