Overhaul project structure, developer workflow, and documentation

[sansiro77]

Summary

This PR introduces a major overhaul of the project's development infrastructure. We have migrated our linting and formatting stack to Ruff, integrated Jupytext for better notebook version control, and established a mandatory pre-commit workflow to ensure long-term code quality and consistency.

Key Changes

1. Breaking Changes

• Class Rename: In the Photonic module, the class GBS_Graph has been renamed to GraphGBS.

2. Tooling & Infrastructure

• Integrated Ruff: Replaced Pylint with Ruff for lightning-fast linting and formatting.
• Jupytext Integration: Established paired .ipynb and .py:percent files for tutorials and examples to allow cleaner git diffs.
• Pre-commit Hooks: Added .pre-commit-config.yaml to automate:
  • Code linting and formatting (Ruff).
  • Notebook synchronization (Jupytext).
  • General file sanity checks (trailing whitespace, EOF).

3. Documentation & Standards

• CONTRIBUTING.md: Created a comprehensive guide for new contributors.
• README.md: Updated with modern developer setup instructions and badges.
• Docstring Standard: Enforced Google-style docstrings in the src/ directory via ruff.toml.
• Tutorials Overhaul: Reorganized file paths and updated titles for better navigation.