refactor: restructure repo into thematic directories v3.1.0

Major repository reorganization for improved navigation:

New directory structure:
- guide/ - Core documentation (ultimate-guide, cheatsheet, adoption)
- tools/ - Interactive utilities (audit, onboarding, mobile-access)
- machine-readable/ - LLM/AI consumption (reference.yaml, llms.txt)
- exports/ - Generated outputs (PDFs)

Changes:
- Move 10 files to thematic directories with cleaner names
- Create README.md index for each new directory
- Update 150+ internal links across all documentation
- Add "Repository Structure" section to main README
- Remove redundant npm install command from README header
- Remove unverified cost estimate from prerequisites
- Fix broken anchor link (#-quick-start-15-minutes)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

machine-readable/README.md

@@ -0,0 +1,33 @@
+# Machine-Readable References
+
+Files optimized for LLM/AI consumption.
+
+## Contents
+
+| File | Description | Tokens |
+|------|-------------|--------|
+| [reference.yaml](./reference.yaml) | Structured index with line numbers for deep dives | ~2K |
+| [llms.txt](./llms.txt) | Standard LLM context file for repository indexation | ~1.5K |
+
+## Usage
+
+### Give Claude Code instant expertise
+
+```bash
+# Paste into any AI assistant
+curl -sL https://raw.githubusercontent.com/FlorianBruniaux/claude-code-ultimate-guide/main/machine-readable/reference.yaml
+```
+
+### Reference in Claude Code
+
+```
+@machine-readable/reference.yaml
+```
+
+### Add to system prompts
+
+Include the YAML content in your AI assistant's system prompt for Claude Code expertise.
+
+---
+
+*Back to [main README](../README.md)*