Cardano Updates

refactor(build): migrate to PEP 621 and pyproject.toml only

pyrefly does not handle editable installs and adds 'cardano_clusterlib'
to 'project-excludes' by default. To ensure proper checking, explicitly
add 'cardano_clusterlib' to the args list in the pre-commit config.

Switch build configuration from setup.py/setup.cfg to PEP 621-compliant
pyproject.toml. Update setuptools and setuptools_scm requirements, move
package metadata and configuration to pyproject.toml, and remove legacy
setup.py and setup.cfg files. This modernizes the build process and
improves compatibility with current Python packaging standards.

chore: update linting, CI, and dependencies

- Rename and update GitHub Actions workflow to `repo_tests`, using Python 3.12,
  venv, and improved pre-commit caching and activation.
- Update pre-commit config: bump ruff and markdownlint versions, move pyrefly
  hook, and update ruff hook id.
- Update Makefile to require virtualenv for pip installs and improve commands.
- Bump mypy and pyrefly versions in requirements-dev.txt.
- Minor code cleanups: remove obsolete pyrefly ignore comments, clarify variable
  names, and use context manager for subprocess in docs conf.py.