Update cookiecutter template

[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.
• CHANGES.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 to the latest commit
• Addresses a handful of misconfigurations in the workflows
• Updates ruff to v0.2.0 and black to v24.2.0

Does this PR introduce a breaking change?

No.

Other information:

The cache-cleaner.yml workflow was missing a key permission to run properly. This is now fixed.