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
begining improve the rake task for categories
rake task loads ontology from ontohub.org

if it loads nessecery and imports it into the meta
 repository. and it generates the categories
remove non needed variable and method call
Add SaveOptions to reduce arguments of save_ontology