add create_version method
add create_ontology method

Conflicts:
	app/models/repository/git_repositories.rb
remove iri argument
simplify ontology retrieval
make user argument mandatory
rename variable
add do_not_parse to save_file
fix version having wrong path bug
move tests to rspec
further simplification
Refactor files action of FilesController

Introduce service object RepositoryFile which
contains the logic of file and directory
retrieval on model level.

Introduce GitFile which contains logic of
file and directory retrieval on git/lib level.

Those classes separate the concerns of git/lib
and ontohub models way more.

Use InheritedResources for FilesController
and simplify files action (will be renamed later)
split history action off of files controller
fix remaining merge error
fix syntax error
code style
fix MethodMissing error
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.
begining improve the rake task for categories