🔧 Refactor Project Structure

### 🧭 Summary

The current file structure of the `s2dm` project has grown without a consistent layout, making it harder to navigate and extend. We propose a refactor to align with **Python best practices** for CLI-based tools and to improve support for:

- Modular commands
- Reusable business logic
- Documentation generation via Hugo (`docs-gen/`)
- Clean testing and packaging

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### ✅ Goals

- Consolidate all source code inside a proper Python package (`s2dm/`)
- Separate CLI entry points, core logic, and utilities
- Keep `docs-gen/` cleanly separated for Hugo-based documentation
- Improve readability and maintainability of the codebase
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