Remove nbqa in favor of ruff's native Jupyter support (v0.6.0+).
Replace papermill with nbconvert due to uv dependency resolution issues.
Also remove S105/S106 ignores to enforce better security practices.
- Update pyproject.toml to use ruff v0.12.12 with native notebook support
- Replace papermill with nbconvert for notebook execution
- Remove nbqa from all dependencies and pre-commit hooks
- Update GitHub Actions workflows to use ruff directly
- Remove hardcoded password ignores for better security
- Update documentation to reflect simplified setup
- Add dummy package structure for hatchling build system
🤖 Generated with [Claude Code](https://claude.ai/code)
Co-Authored-By: Claude <noreply@anthropic.com>
