Refactor: dataset - use id on all endpoints and cli

[jcace]

closes #64

[jcace]

Requires the following to be run on the DB to migrate:

UPDATE contents
SET dataset_id = (
    SELECT id FROM datasets WHERE name = contents.dataset_name
);

On sqlite:

sqlite3 delta-dm.db 'UPDATE contents SET dataset_id = (SELECT id FROM datasets WHERE name = contents.dataset_name);'