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.
add do_not_parse to save_file

Conflicts:
	app/models/repository/git_repositories.rb
Merge pull request #999 from ontohub/extract_do_not_parse

add do_not_parse to save_file
move db cleaner config to separate file
replace rake task db:purge with db:migrate:clean
remove ontology file extensions stubs
clean redis in minitest-setup
put redis cleanup into a rake task
clean redis before test run
use transaction strategy in rspec
use transaction strategy in minitest and cucumber
suppress warnings and notices about transactions
fix typo
fix cleaning of test database
add comment on Rake::Task.overwrite/abandon
Merge pull request #915 from ontohub/855-proper_database_cleaning

855 proper database cleaning
fix form-fields for names yet again.
change source/target form to explicitly to string.