Update assorted gems

Here is a list produced by bundle update:
Updating git://github.com/tristanm/jstree-rails.git
Updating git://github.com/digineo/sunspot.git
Updating git://github.com/llwt/codemirror-rails.git
Updating git://github.com/0robustus1/ontology-united.git
Installing coffee-script-source 1.7.1 (was 1.7.0)
Installing i18n 0.6.11 (was 0.6.9)
Installing tzinfo 0.3.40 (was 0.3.39)
Installing execjs 2.2.1 (was 2.2.0)
Installing netrc 0.7.7
Installing diffy 3.0.6 (was 3.0.4)
Installing ice_cube 0.12.1 (was 0.12.0)
Installing slop 3.6.0 (was 3.5.0)
Installing rdf 1.1.4.3 (was 1.1.4)
Installing redis 3.1.0 (was 3.0.7)
Installing rspec-core 2.99.1 (was 2.99.0)
Installing rspec-mocks 2.99.2 (was 2.99.1)
Installing faker 1.4.2 (was 1.3.0)
Installing simplecov 0.9.0 (was 0.8.2)
Installing compass 0.12.7 (was 0.12.6)
Installing rspec-expectations 2.99.2 (was 2.99.0)
Installing coffee-script 2.3.0 (was 2.2.0)
Installing uglifier 2.5.3 (was 2.5.1)
Installing rubydns 0.8.5 (was 0.8.4)
Installing rest-client 1.7.2 (was 1.6.7)
Installing redis-namespace 1.5.1 (was 1.4.1)
Installing cucumber 1.3.16 (was 1.3.15)
Installing shoulda-matchers 2.6.2 (was 2.6.1)
Installing pry-byebug 1.3.3 (was 1.3.2)
Installing sidekiq 3.2.1 (was 3.1.4)
Installing capistrano-bundler 1.1.3 (was 1.1.2)
Installing acts_as_tree 2.0.0 (was 1.6.1)
Installing sidekiq-failures 0.4.3 (was 0.4.2)
Installing d3_rails 3.4.10 (was 3.4.8)
Installing jquery-rails 3.1.1 (was 3.1.0)
Installing jquery-ui-rails 5.0.0 (was 4.2.1)
Installing momentjs-rails 2.8.1 (was 2.7.0)
Installing quiet_assets 1.0.3 (was 1.0.2)
Installing nokogiri 1.6.3.1 (was 1.6.2.1)
Installing capybara 2.4.1 (was 2.3.0)

The 'using' lines were removed.
conform to new jquery-ui filenames

With 5.0.0 the jquery-ui rails gem
changed their filenaming scheme, this should
take care of our includes.
be safe through twiddle-wakka version operator

The twiddle-wakka version operator in the Gemfile should keep us safe of
unexpected major version upgrades.

See http://robots.thoughtbot.com/rubys-pessimistic-operator for more
twiddle-wakka information.
remove unused gems

diffy, byebug and pry-byebug were removed
as gem-dependencies as we do not currently use
them or plan to use them in the near future.
Merge pull request #997 from ontohub/fix_outdated_by_updating_gems

Update assorted gems