Remove top level Rugged from the Gemfile

Note; the rugged gem is still pulled in as a dependency for Licensee but is never used.

What are the relevant issue numbers?

None, as of right now.

Does this MR meet the acceptance criteria?

• Changelog entry added, if necessary
• Documentation created/updated
• Tests added for this feature/bug
• Conforms to the code review guidelines
• Conforms to the merge request performance guidelines
• Conforms to the style guides
• Conforms to the database guides