utils/gems: don't run `bundle clean`.

[MikeMcQuaid]

This (incorrectly) removes gems that are also part of the system Ruby e.g. base64 which contradicts warnings from Ruby itself when requireing these gems.

Extracted from #17342 as this needs to be in master for that PR's vendored gems job to pass.

[Bo98]

bundle install will just do the same though so this doesn't fix it.

[MikeMcQuaid]

Passing on this for now.