Run the following under internal execution inside
NetBeans. You will get a NullPointerException like
the one that follows. The problem is that
AEIndexSetWrapper.clear() is calling
IndexSetWrapper.wrap() with a null argument. This
causes IndexSetWrapper.wrap() to return null.
Then, this null result is given to
AEIndexSetWrapper.remove() and then also given to
AssocEndIndexSet.checkType(). checkType throws the
NullPointerException explicitly when it finds its
argument is null.

Note that this seems to only happen when the whole
extent is deleted. If you change the
pkgA.refDelete() to p.refDelete() then there is no
NullPointerException.

This affects the <mof> Ant task I wrote but I was
able to work around it by simply doing the
.clear() before the .refDelete() of the extent.

import org.netbeans.api.mdr.*;
import javax.jmi.model.*;

public class EmptyReferenceTest {
    public static void main(String [] s) throws
CreationFailedException {
        MDRepository repository =
MDRManager.getDefault().getDefaultRepository();
        ModelPackage pkgA = (ModelPackage)
repository.createExtent("A");
        ModelPackage pkgB = (ModelPackage)
repository.createExtent("B");
        MofPackage p =
pkgA.getMofPackage().createMofPackage();
        Constraint c =
pkgB.getConstraint().createConstraint();
        c.getConstrainedElements().add(p);
        //p.refDelete();
        pkgA.refDelete();
        c.getConstrainedElements().clear();
    }
}

=>

java.lang.NullPointerException
        at
org.netbeans.mdr.storagemodel.AssocEndIndexSet.checkType(AssocEndIndexSet.java:73)
        at
org.netbeans.mdr.handlers.AEIndexSetWrapper.remove(AEIndexSetWrapper.java:111)
        at
org.netbeans.mdr.handlers.AEIndexSetWrapper.clear(AEIndexSetWrapper.java:51)
        at
EmptyReferenceTest.main(EmptyReferenceTest.java:13)
        at
sun.reflect.NativeMethodAccessorImpl.invoke0(Native
Method)
        at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at
java.lang.reflect.Method.invoke(Method.java:324)
        at
org.openide.execution.ThreadExecutor.executeClass(ThreadExecutor.java:117)
        at
org.openide.execution.ThreadExecutor$TERunnable.run(ThreadExecutor.java:184)
        at
org.netbeans.core.execution.RunClassThread.run(RunClassThread.java:118)