reproducible debian: sqla, wrap all queries into transactions

this saves me the effort of figuring out how 2.0 triggers

    sqlalchemy.exc.InvalidRequestError: This connection has already initialized a SQLAlchemy Transaction() object via begin() or autobegin; can't call begin() here unless rollback() or commit() is called first.

in scheduler.

While doing that, I can also drop some manual begin/commit that were
being done in the scheduler.

Signed-off-by: Mattia Rizzolo <mattia@debian.org>