chore: security hardening, documentation restoration, and full test suite

[yss-ef]

Summary

This Pull Request synchronizes the latest hardening and documentation work from the dev branch into main.

Key Changes

• Security Hardening: Resolved CodeQL security alerts regarding redundant variable assignments and ineffective statements.
• Robust Error Handling: Updated all empty except blocks to handle specific exceptions (OSError, YAMLError, etc.) with explanatory comments.
• Documentation Restoration: Re-introduced the COMMANDS.md reference and professional README.md overhauled by the doc-writer.
• Test Suite Completion: Restored the comprehensive integration test suite (60 tests total) verifying all 11+ supported stacks.
• Linting Compliance: All files are now 100% compliant with ruff check and formatting standards.

Verification

• 60/60 tests passed.
• Ruff check passed.
• All CodeQL alerts cleared locally.