adjust parse-specs for ontology_version_id check.
handle local files for external repository

Probably only needed in tests, but may prove
useful for other usecases too.
set ontology_version_id always.
create update_version! method and use it

This includes setting the version, if a new version
is created through the update_version controller action.

Also compact is used on versions before iterating to
filter out nil-values (result of versions.current being nil on some
test-ontologies).
define current_version method and use it

current_version will use ontology_version, but will
fallback to versions.current if necessary.
Merge pull request #894 from ontohub/232-use_ontology_version_id

232 use ontology version