Use bundler to install Omnibus gems

Instead of calling `gem install <x>` many times, let's define the
`Gemfile` and `Gemfile.lock` and run `bundle install`. This ensures
dependencies are pinned and don't quietly move with a new invocation
of `gem install`. There is also a side benefit to using `bundler`: we
can later use the newly-introduced feature to include and verify
checksums (ruby/rubygems#6374).

`bundler` generally installs everything in the expected gem directory
 that is used by `ruby`, but for gems installed from a Git source,
`bundler` puts those gems in a special `bundler/gems` directory.
We don't use any gems from Git sources now--`gitlab-ruby-shadow`
is now used instead of `ruby-shadow`--there is no issue.

Also, note that if we want to ensure `gitlab-ctl` doesn't try to pull
in gems from GitLab Rails, we could invoke `bundler`, but this is a
slightly riskier change.

Relates to https://gitlab.com/gitlab-org/omnibus-gitlab/-/issues/8368

Changelog: changed

Author: stanhu