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
fix typo
fix cleaning of test database
add comment on Rake::Task.overwrite/abandon
Merge pull request #915 from ontohub/855-proper_database_cleaning

855 proper database cleaning
fix form-fields for names yet again.
change source/target form to explicitly to string.