[source/native] refactor eid generation code This set of related methods clutters the native source API. It will be better served with a dedicated eid genrator object. Related to #3526594. [jcr: allocate the eid generator in __init__]

sql('DROP TABLE "deleted_entities"')
sql('ALTER TABLE "entities" DROP COLUMN "mtime"')
sql('ALTER TABLE "entities" DROP COLUMN "source"')