Enhance Setup Script with Environment Variables

[pyang4s]

Description:
Improve security by supporting environment variables instead of hardcoded credentials in database.yml.

Acceptance Criteria:

• Modify scripts/setup.sh to check for environment variables first
• Fall back to database.yml if env vars not set
• Create .env.example file with template
• Update setup.sh to use .env file if present
• Add .env to .gitignore
• Document environment variable usage in README
• Update notebooks to support env vars

Estimated Effort: 2-3 hours