Revert "Use active scope for retrieving repositories."

This reverts commit d053813dcf22b74cded34daf5734e54388e9bee6.

Conflicts:
	app/controllers/home_controller.rb
	app/controllers/ontology_search_controller.rb
	app/helpers/application_helper.rb
	app/models/repository/destroying.rb
Add scopes and default scope, adjust migrations.
Fix errors introduced by default scope.