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00_INDEX.md
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# Documentation Index This directory contains comprehensive documentation for the SciTeX Writer template system. Files are organized with explicit descriptive prefixes for semantic clarity and easy navigation. ## Main Documentation (Root Level) ### Guides (01_GUIDE_*) Procedural documentation for common tasks and workflows: - **01_GUIDE_QUICK_START.md** - Quick reference for common tasks and basic workflows - **01_GUIDE_INSTALLATION.md** - Setup for all environments - **01_GUIDE_BIBLIOGRAPHY.md** - Complete guide to bibliography management with multi-file support and caching - **01_GUIDE_CONTENT_CREATION.md** - Comprehensive guide for creating and managing figures and tables - **01_GUIDE_AGENTS.md** - Guide for using AI agents and LLMs with the system ### Architecture (02_ARCHITECTURE_*) Technical design and implementation details: - **02_ARCHITECTURE_IMPLEMENTATION.md** - System architecture, technical implementation, and troubleshooting guide ### MCP Tools - **MCP_TOOLS.md** - Reference for all 29 MCP tools for AI agent integration ## Subdirectories ### `to_claude/` Configuration and guidelines for Claude Code integration: - **agents/** - Individual agent specifications and responsibilities - **bin/** - Utility scripts and tools - **examples/** - Example projects and workflows - **guidelines/** - Development guidelines organized by topic: - `command/` - Command reference guides - `elisp/` - Emacs Lisp development standards - `programming_common/` - General programming best practices - `project/` - Project-level standards - `python/` - Python-specific guidelines - `science/` - Scientific writing standards - `shell/` - Shell scripting guidelines ### `INSTRUCTIONS_TO_CLAUDE_CODE/` Step-by-step instructions for Claude Code tasks: - Custom Python management - Project structure guidelines - Testing strategies - Shell scripting - Git/GitHub workflows - System information and troubleshooting ### `structure/` - **structure.md** - Directory structure documentation - **structure.mmd** - Mermaid diagram of repository structure ## Navigation Tips 1. **For quick answers**: Start with `01_GUIDE_QUICK_START.md` 2. **For installation**: See `01_GUIDE_INSTALLATION.md` 3. **For bibliography management**: See `01_GUIDE_BIBLIOGRAPHY.md` 4. **For figure/table creation**: See `01_GUIDE_CONTENT_CREATION.md` 5. **For AI agent and LLM setup**: Consult `01_GUIDE_AGENTS.md` 6. **For technical architecture**: Review `02_ARCHITECTURE_IMPLEMENTATION.md` 7. **For MCP tools reference**: See `MCP_TOOLS.md` 8. **For Python development**: Check `to_claude/guidelines/python/` directory 9. **For project management**: Look in `to_claude/guidelines/project/` 10. **For scientific writing standards**: See `to_claude/guidelines/science/` directory ## File Naming Convention Root-level documentation files use explicit descriptive prefixes for semantic meaning: - **01_GUIDE_*** = Guide (procedural, how-to documentation) - `01_GUIDE_QUICK_START.md` - Quick reference for immediate needs - `01_GUIDE_INSTALLATION.md` - Setup for all environments - `01_GUIDE_BIBLIOGRAPHY.md` - Bibliography management and organization - `01_GUIDE_CONTENT_CREATION.md` - Detailed creation processes - `01_GUIDE_AGENTS.md` - AI and LLM integration - **02_ARCHITECTURE_*** = Architecture (technical design and implementation) - `02_ARCHITECTURE_IMPLEMENTATION.md` - System design and technical details This prefix system provides immediate visual context about document purpose and category when viewing directory listings. Subdirectory files within `to_claude/guidelines/` use numbered prefixes when they represent sequential steps or priority levels (e.g., `01_DEVELOPMENT_CYCLE.md`, `02_NAMING_CONVENSIONS.md`).