It looks like javax.transaction is no longer in /lib. That caused me a few minutes of panic while upgrading from M3 to M6 right now. javax.transaction.Transaction manager could not be resolved from org.springframework.orm bundle.
javax.transaction is in a list of org.osgi.framework.system.packages in java6-server.profile. I manually copied javax.transaction to lib and restarted and was back in a good graces of osgi gods.
The question is - should java6-server.profile be modified as well to remove javax.transaction from the list of system packages?
I did just that, removed all references to javax.transaction from java6-server.profile and deleted javax.transaction from lib and now bundles deployed in the userregion properly resolve to the javax.transaction bundle deployed in repository/ext.