tools-only 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 | Main entry point, quick start, features overview | Everyone | v2.7.0 |
| docs/README.md | Documentation hub with navigation guide | Everyone | v2.7.0 |
| CHANGELOG.md | Version history and release notes | Everyone | v2.7.0 |
User Guides
| Document | Content | When to Read |
|---|---|---|
| FEATURES.md | Complete feature guide (document generation, AI capabilities, file integration) | To understand what's possible |
| SKILLS.md | All 19+ skills with examples | To learn available capabilities |
| API.md | Programmatic API reference with code examples | When using Python API |
| TROUBLESHOOTING.md | Common issues and solutions | When you encounter problems |
Developer Resources
| Document | Content | Audience |
|---|---|---|
| DEVELOPMENT.md | Architecture, plugin development, contributing | Contributors, maintainers |
| RELEASING.md | Version management, PyPI publishing | Maintainers |
| example_api_usage.py | Working Python examples | API users |
| TESTING_INSTRUCTIONS.md | Plugin testing guide | Plugin developers |
System Documentation
| Document | Content | Audience |
|---|---|---|
| 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):
- Start: Plugin Installation Guide
- Reference: Skills Overview
- Troubleshoot: Plugin Issues
As a CLI Tool:
- Start: Installation → CLI Usage
- Reference: Common Commands
- Troubleshoot: CLI Issues
As a Python API:
- Start: API Quick Start
- Reference: API Documentation
- Examples: example_api_usage.py
I Want to Generate Specific Documents
| Document Type | Getting Started | Detailed Guide | Examples |
|---|---|---|---|
| Research Papers | Quick Start | Features: Papers | README Examples |
| Grant Proposals | Grant Commands | Skills: Grants | Features: Grants |
| Research Posters | Poster Commands | Skills: Posters | Features: Posters |
| Clinical Reports | Clinical Commands | Skills: Clinical | Features: Clinical |
| Literature Reviews | Review Commands | Skills: Literature | Features: Reviews |
| Presentations | Slides Examples | Skills: Slides | CLAUDE.md: Presentations |
I Want to Use Specific Features
| Feature | Documentation | Skills Involved |
|---|---|---|
| Research Lookup | Features: Research Lookup | research-lookup |
| Peer Review | Features: Peer Review | peer-review, scholar-evaluation |
| Citation Management | Skills: Citations | citation-management |
| Document Conversion | Features: Conversion | markitdown |
| Scientific Schematics | Features: Schematics | scientific-schematics |
I Want to Develop or Contribute
Plugin Development:
- Plugin Structure
- Local Testing
- Testing Guide
Python Package Development:
- Architecture
- Setup
- Contributing
Publishing:
- Version Management
- Publishing to PyPI
- Verification
🔗 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
- 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)
- Read: Main README (5 min)
- Install: Follow Plugin Installation (2 min)
- Try: Create your first document (10 min)
- Explore: Browse Skills Overview (10 min)
Intermediate Path (Regular Users)
- Master: Common Commands
- Learn: Research Lookup
- Use: Peer Review
- Optimize: File Integration
Advanced Path (Power Users)
- API: Read API Reference
- Customize: Understand System Instructions
- Extend: Learn Plugin Development
- Contribute: Follow Contributing Guide
📝 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:
- Check: Troubleshooting Guide
- Search: GitHub Issues
- Report: Create a new issue with the "documentation" label
- Discuss: Join our Slack Community
Last Updated: January 22, 2025 (v2.7.0)
Documentation Status: ✅ Complete and Current