feat(db-manager): remove addCollection and addFragment functions

BREAKING CHANGE: If you were relying on db-manager to add collections and fragments, this will no longer work. Since Collections and Fragments are now merely model components (previously part of core), on equal footing with the rest of the model components, the recommended migration path is to use your own seed script, e.g. https://gitlab.coko.foundation/pubsweet/pubsweet-starter/blob/master/scripts/seed.js to perform database setup/seed.