This increases data inconsistency and also performance of the whole
update process: SqlAlchemy can use its own caching better with a single
transaction as it does not need to mark already fetched objects as dirty
and so re-fetch them again on later use. So after deleting a domain,
we can still use the previously fetched domain objects for the update
operations afterwards. Otherwise SqlAlchemy had to fetch each domain
object again with single SELECT statements which leads to bad
performance with many domains (>> 1000).

The introduced "do_commit" variable controls whether the database
changes are to be committed by the caller or in the called method
itself. So we can use a single transaction for the Domain.update()
method while still preserving the previous behavior for other callers.

Closes #428.