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.