Fix prune-old-flaky-examples by specifying RubyGems source

What does this MR do and why?

Follow-up of !126074 (merged).

By specifying the gems source in the inline Gemfile in scripts/flaky_examples/prune-old-flaky-examples, the update-tests-metadata job pass again (without having to manually install rspec: https://gitlab.com/gitlab-org/gitlab/-/jobs/4641122044

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