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ATM we only have one global transaction manager which is ok for 1 jdo-conf, but if we load 2 different jdo-conf's they can have different definitions for transaction managers. IMO we will need to assign a ConnectionFactory with the transaction manager that will handle its transactions.
I agree with Ralf that we need to re-assess some of the old assumptions in the light of multiple JDO configurations. This, imho, should be done in a separate Jira issue to be created.
Actually, we should even reconsider whether the 1:m relation between transaction mode and databases instances is justified.