BACKPORT-16-10-stable: Use bundler to install Omnibus gems

What does this MR do?

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 (https://github.com/rubygems/rubygems/pull/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 #8368

Changelog: changed

Related issues

Relates to Isolate Omnibus dependencies from GitLab Rails ... (#8368) • Unassigned

Checklist

See Definition of done.

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Required

• MR title and description are up to date, accurate, and descriptive.
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For GitLab team members

If you don't have access to this, the reviewer should trigger these jobs for you during the review process.

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Expected (please provide an explanation if not completing)

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• Tests added.
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