Update cookiecutter template, minor fixes

[Zeitsperre]

Pull Request Checklist:

• This PR addresses an already opened issue (for bug fixes / features)
  • This PR fixes #xyz
• (If applicable) Documentation has been added / updated (for bug fixes / features).
• (If applicable) Tests have been added.
• CHANGELOG.rst has been updated (with summary of main changes).
  • Link to issue (:issue:number) and pull request (:pull:number) has been added.

What kind of change does this PR introduce?

• Updates the cookiecutter template
• Python and GitHub Actions version updated
• Now using advanced CodeQL configuration
• New pre-commit hooks vulture (find dead code), codespell (grammatical errors), zizmor (workflow security), and gitleaks (token commit prevention).
• Corrected some spelling and security issues
• Removed the Python netcdf4 package.

Does this PR introduce a breaking change?

Nope.

Other information:

mypy is staged but not configured. This will require a significant amount of effort to adopt and adhere to.

[Zeitsperre]

@coxipi Do you happen to know what could be the cause of problems here? I'm seeing segfaults (?!) on conda builds.

[coxipi]

That looks goodf