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.
Merge pull request #1006 from ontohub/fix_push_but_no_ontologies2

Fix push but no ontologies2
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
move persisted? method to fakerecord
simplify target_path
add RepositoryDirectory FakeRecord
Add view for RepositoryDirectory
add DirectoriesController
Fix target_path methods (leading slash not allowed)
fix validation in RepositoryDirectory
activate directory creation
add comment on class purpose
use more delegates, remove redundant code
simplify committing mechanics
configure rspec mocks
fix specs on ontology deletion
Merge branch '961-folder_creation' into develop