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When some GUI code tries to access the Repository, the AWT thread blocks up on MDR initialization which takes some time. I suggest that the MDR module API allows to start the initialization asynchronously and obtain an initialization Task (org.openide.util.Task), which can be waited on and which sends out an event when the initialization is complete.
This is a problem - very likely it is not a repository initialization that takes the time - it is any JMI call that touches the repository for the first time. The first request to a repository extent is slower because the storage does not have anything in its cache yet. Repository bootstrap is an exception - it probably can be done on some other thread, however repository boots very rarely, so I changed the priority of this issue to P4.
see above reasons