Tidy up Gemfile

This removes some unused/unnecessary gems and also removes staging
from the development/test group.

brakeman - is an independent gem that doesn't need to be loaded in-app
boomerang_rails - no longer used
rails-dev-boost - recent versions of Rails make this redundant
crack - webmock now uses a safe version
minitest - Ruby 1.9.3 ships with version 2.5.1 already