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Once the ability is added to make metadata modifications at runtime, MOXy will need to ability to persist the metadata in some form (oxm.xml, other representation?). This is so that if the JAXBContext is part of an application that the metadata can survive the application being restarted.
Instead of changes being made at runtime that need to be persisted, changes will be made externally and the JAXBContext will be refreshed: Bug 343615 - Enhancement: Add ability to refresh JAXBContext based on metadata changes https://bugs.eclipse.org/343615
The Eclipselink project has moved to Github: https://github.com/eclipse-ee4j/eclipselink