chore: organize repository structure and protect sensitive data

## Repository Organization

### Security Improvements
- Update .gitignore with comprehensive patterns for sensitive files
- Protect API keys in .env (never committed to git)
- Create detailed .env.example template without real keys
- Archive .env.gemini-primary to .backup/ (git-ignored)
- Add SECURITY.md with key management guidelines
- Add FINAL_SECURITY_REPORT.md with complete audit

### File Organization
- Move 30+ documentation files to docs/ directory
- Move 20+ test files to tests/ directory
- Archive 40+ log files to .backup/ (git-ignored)
- Clean root directory from 60+ to 24 items
- Create docs/README.md with documentation index
- Create .backup/README.md explaining archived content

### Documentation
- Add NEXT_STEPS.md with clone and setup instructions
- Add ORGANIZATION_SUMMARY.md with complete change log
- Update .env.example with professional template
- Enhance .gitignore with 15+ security patterns

### Cleanup
- Remove coverage files (.coverage*)
- Remove empty log files
- Remove backup versions of code files
- Organize project structure for better maintainability

### Changes Summary
- 50 files changed
- 289 insertions, 13,344 deletions
- Zero sensitive data exposed
- Ready for git clone on other machines

🤖 Generated with [Claude Code](https://claude.com/claude-code)

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

Author: JuanCS-Dev

.coverage.juan-Linux-Mint-Vertice.100206.XatiVRdx

@@ -1,25 +1,61 @@
-# LLM Provider API Keys (REQUIRED - Choose at least one)
-HF_TOKEN=your_huggingface_token_here
-NEBIUS_API_KEY=your_nebius_api_key_here
+########################################
+# QWEN DEV CLI - Environment Configuration
+# SECURITY WARNING: NEVER commit .env files!
+########################################
+
+# ===========================================
+# PRIMARY LLM PROVIDER (Choose One)
+# ===========================================
+LLM_PROVIDER=gemini
+# Options: gemini | ollama | nebius | huggingface
+
+# ===========================================
+# GEMINI API (Google AI) - RECOMMENDED
+# ===========================================
 GEMINI_API_KEY=your_gemini_api_key_here
+GEMINI_MODEL=gemini-2.5-flash
+# Get your key: https://makersuite.google.com/app/apikey
+# Models: gemini-2.5-flash, gemini-1.5-pro, gemini-1.0-pro
+
+# ===========================================
+# OLLAMA (Local LLM) - FREE & PRIVATE
+# ===========================================
+OLLAMA_BASE_URL=http://localhost:11434
+OLLAMA_MODEL=qwen2.5-coder:latest
 OLLAMA_ENABLED=false
+# Install: https://ollama.ai
+# Models: qwen2.5-coder:latest, codellama, deepseek-coder
 
-# Model Configuration
+# ===========================================
+# NEBIUS AI (Alternative Cloud Provider)
+# ===========================================
+NEBIUS_API_KEY=your_nebius_api_key_here
+# Get your key: https://nebius.com
+
+# ===========================================
+# HUGGINGFACE (Inference API)
+# ===========================================
+HF_TOKEN=your_huggingface_token_here
 HF_MODEL=Qwen/Qwen2.5-Coder-7B-Instruct
-GEMINI_MODEL=gemini-pro
+# Get your token: https://huggingface.co/settings/tokens
+
+# ===========================================
+# MODEL CONFIGURATION
+# ===========================================
 MAX_CONTEXT_TOKENS=32768
 
-# Optional Features
+# ===========================================
+# GRADIO UI (Optional Web Interface)
+# ===========================================
 GRADIO_PORT=7860
 GRADIO_SHARE=false
 
-# Instructions:
-# 1. Copy this file to .env: cp .env.example .env
-# 2. Fill in your API keys (at least one)
-# 3. Run: qwen shell
+# ===========================================
+# SETUP INSTRUCTIONS
+# ===========================================
+# 1. Copy this file: cp .env.example .env
+# 2. Edit .env and add your API key(s)
+# 3. Never commit .env to git!
+# 4. Run: qwen shell
 #
-# API Key Sources:
-# - HuggingFace: https://huggingface.co/settings/tokens
-# - Nebius: https://nebius.com
-# - Gemini: https://makersuite.google.com/app/apikey
-# - Ollama: Local installation (ollama.ai)
+# For more info: https://github.com/yourusername/qwen-dev-cli

.coverage.juan-Linux-Mint-Vertice.100592.Xirhmcax

@@ -44,18 +44,52 @@ htmlcov/
 .mypy_cache/
 .ruff_cache/
 
-# Environment
+# Environment Variables (SENSITIVE - NEVER COMMIT)
 .env
+.env.*
+!.env.example
 .env.local
+.env.backup
 *.log
+*.key
+*.pem
+*.p12
+credentials.json
+secrets/
+.secrets/
 
 # Temporary files
 *.tmp
 *.bak
+*.backup
+*_backup*
+*.swp
+*.swo
 temp/
 tmp/
 
 # Project specific
 .qwen_backups/
+.backup/
 test_results.log
-=6.0.0
+.qwen_history
+
+# Test artifacts and logs
+test_*.log
+*.coverage*
+htmlcov/
+.pytest_cache/
+
+# IDE and OS
+.DS_Store
+.vscode/
+.idea/
+*.sublime-*
+
+# Documentation (temporary - will organize)
+*_REPORT.md
+*_SUMMARY.md
+TESTE_*.md
+test_*.py
+maestro_v*.py
+!maestro_v10_integrated.py