Ensure ruby runtime does not contain duplicated gems

[donoghuc]

Logstash artifacts contain both a jruby interpreter as well as a gem environment including dependencies and plugin gems. The gem environment is managed via bundler. Jruby ships with a collection of "default" gems https://github.com/jruby/jruby/blob/master/lib/pom.rb just like MRI ruby. When a gemspec contains an explicit dependency on a default gem, bundler will try to fetch the latest version from rubygems. In the case where there is a newer version than the default shipped with jruby an ambiguous gem loading warning will be surfaced.

Examples:

• Unresolved or ambiguous specs during Gem::Specification.reset: date (>= 0) #16095
• Running bin/logstash will produce a Gem::Specification.reset warning on startup #16754

The interim solution for resolving these issues has been to explicitly pin gems to the version shipped in jruby #16755

This solution requires manual intervention and is prone to missing required updates. We should build a better solution for resolving conflicts between gems managed with bundler and those shipped with jruby.

Desired outcomes

• At minimum we should automate at least checking for conflicts periodically.
• Come up with a solution for managing this, if it is just pinning explicitly come up with a way to automate that workflow

Another thing to consider may be something like:

# Force bundler to prefer gems from rubygems.org over default gems
source "file://#{JRUBY_DIR}/lib/ruby/gems/shared" do
  gem 'date', '3.3.3'
end