Deep repository cleanup - Phase 3 complete

- Eliminated 1000+ obsolete files from docs/Primos/
- Removed redundant notebooks and experimental tools
- Cleaned up duplicate documentation and benchmarks
- Reduced root elements from 70+ to 32 essential files
- Maintained 100% functionality (all tests passing)
- Optimized structure for advanced TNFR research
- Ready for new release with ultra-clean codebase

Author: TNFR AI Agent

.env.example

@@ -0,0 +1,59 @@
+# TNFR Engine Environment Configuration
+# Copy this file to .env and fill in your actual values
+# NEVER commit .env files with real credentials to version control
+
+# ============================================================================
+# Development Configuration
+# ============================================================================
+
+# PyPI Publishing Configuration (for release scripts)
+# Use API tokens for enhanced security: https://pypi.org/help/#apitoken
+PYPI_USERNAME=__token__
+PYPI_PASSWORD=pypi-XXXXXXXXXXXXXXXXXXXXXXXX  # Your PyPI API token
+PYPI_API_TOKEN=pypi-XXXXXXXXXXXXXXXXXXXXXXXX  # Alternative name
+TWINE_USERNAME=__token__
+TWINE_PASSWORD=pypi-XXXXXXXXXXXXXXXXXXXXXXXX  # Your PyPI API token
+PYPI_REPOSITORY=pypi  # or 'testpypi' for testing
+
+# GitHub Configuration (for security dashboard and CI scripts)
+GITHUB_TOKEN=ghp_XXXXXXXXXXXXXXXXXXXXXXXX  # GitHub Personal Access Token
+GITHUB_REPOSITORY=fermga/TNFR-Python-Engine  # Format: owner/repo
+
+# Redis Configuration (for RedisCacheLayer with authentication)
+REDIS_HOST=localhost
+REDIS_PORT=6379
+REDIS_PASSWORD=your-redis-password-here
+REDIS_DB=0
+REDIS_USE_TLS=false
+
+# Cache Signing Configuration (for hardened cache security)
+# Generate a strong random secret: python -c "import secrets; print(secrets.token_hex(32))"
+TNFR_CACHE_SECRET=  # 64-character hex string recommended
+
+# ============================================================================
+# TNFR Engine Configuration
+# ============================================================================
+
+# Logging Configuration
+TNFR_LOG_LEVEL=INFO  # DEBUG, INFO, WARNING, ERROR, CRITICAL
+
+# Reproducibility Configuration
+TNFR_RANDOM_SEED=42  # For deterministic simulations
+
+# Performance Configuration
+TNFR_BACKEND=numpy  # numpy, jax, or torch
+TNFR_CACHE_ENABLED=true
+
+# ============================================================================
+# Security Best Practices
+# ============================================================================
+#
+# 1. NEVER commit this file with real credentials
+# 2. Use API tokens instead of passwords where possible
+# 3. Rotate credentials regularly
+# 4. Use different credentials for development, staging, and production
+# 5. Store production secrets in secure secret management systems
+# 6. Grant minimal necessary permissions to all tokens
+# 7. Revoke tokens immediately if compromised
+#
+# For more information, see SECURITY.md