cleanup: do Session.add directly inside _create_default_perms

Let the various _create_default_perms functions add the created object
to the SQLAlchemy database session, instead of having the caller do it.

This is in accordance with the Kallithea contribution guidelines:

When creating an object using a factory function (like create_repo),
the returned object has already (by convention) been added to the
session, and should not be added again.