ci: Improved security on workflows.

[Jaskowicz1]

This PR changes the security on the workflows to follow GitHub's security workflow for permissions. This PR does not change the following pages:

• ci.yml (not enough information nor testing to see if this will work)
• codeql.yml (permissions already exist here)
• dependency-review.yml (permissions already exist here)
• scorecard.yml (permissions already exist here)

Documentation change checklist

• My documentation changes follow the same style as the rest of the documentation and any examples follow the coding style guide.
• I tested that my change works before raising the PR (via running doxygen, and testing examples).
• I have not moved any existing pages or changed any existing URLs without strong justification as to why.
• I have not generated content using AI or a desktop utility such as grammarly.

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[Jaskowicz1]

Removed documentation.yml from the PR description after discussions with Brain in the Discord server. Made a new push to add top-level permissions.