handle non-existence during timeout

If an ontology version can't be found it probably does not exist, so we
can't timeout on it.
declare queues for workers explicitly.
let god start sequential worker(s).
update usage of ontology-united with vars.
Merge pull request #980 from ontohub/fix_update_the_usage_of_ontology_united

update usage of ontology-united with vars.
change determination of final state for timeout.
Merge pull request #994 from ontohub/fix_by_explicitly_declaring_queues

declare queues for workers explicitly.
Merge pull request #995 from ontohub/fix_working_on_sequential_queue

let god start sequential worker(s).
Merge pull request #993 from ontohub/899-do_not_fail_on_non_existence

899 do not fail on non existence
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