How to prevent JAXB from writing unused namespaces during marshalling

As far as I know, this is indeed not possible in JAXB - and is actually a well-known issue. As you have noticed it, the list of produced namespaces are the ones that have been registered in your JAXBContext, and not the ones that are effectively used when marshalling :-(

I the past, I used the same workaround as you (identify the various used classes and narrow the JAXBContext to this limited set of classes).

Another typical workaround is a 2-step processing: a first marshalling with JAXB, followed by a XSLT transformation to get rid of let's says "polluting" namespaces.

This may not be possible as while marshaling of this objects hierarchy happen, at the time of creating root tag, information about which objects are null v/s not null may not be available. Any attempt to get this information in advance may also have side-effects associated with it as respective accessor methods are invoked. Hence JAXB will statically use info from JAXBContext to have this information populated.

You can try using a different javax.xml.bind.Marshaller implementation.

For example org.eclipse.persistence.jaxb.JAXBMarshaller implementation deals well with this case and remove all unnecessary namespaces when marshall the object.

To do so you need to do the next steps:

• Add eclipselink-2.6.5.jar to the classpath in order to use the org.eclipse.persistence.jaxb.JAXBMarshaller. If you're using gradle you can add compile 'org.eclipse.persistence:eclipselink:2.6.5' to your dependencies.
• Create a jaxb.properties file in the same package where you've the objects to marshall (following the example in your question - JAXBContext c = JAXBContext.newInstance(Foo.class, Bar.class, User.class);, in the package of one of these classes Foo, Bar or User).
• In the jaxb.properties file, add the follow property which specify the desired Context factory:

javax.xml.bind.context.factory=org.eclipse.persistence.jaxb.JAXBContextFactory 

Doing this, the org.eclipse.persistence.jaxb.JAXBMarshaller will be used as a javax.xml.bind.Marshaller implementation on Runtime. And then no unnecessary namespaces will appear when you marshall the objects.