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
Add SaveOptions to reduce arguments of save_ontology
reintroduce ontology-parsing transaction

Seems during the move to the new parsing system
we forgot to also use a main transaction again.
fill child-version with all necessary parent info

The versions of child-ontology should contain
the same data as the corresponding parent version.
This especially includes the commit-oid.
add parent to ontology-version

Also set the parent accordingly during parsing.