Also seeing a ClassCastException with this PDF file.

To reproduce:

• Add a Text Annotation to the page.
• Minimize the popup.
• Click and drag the annotation, the following error is thrown:
  Exception in thread "AWT-EventQueue-0" java.lang.ClassCastException: org.icepdf.core.pobjects.annotations.LinkAnnotation cannot be cast to org.icepdf.core.pobjects.Reference
  at org.icepdf.core.pobjects.Page.updateAnnotation(Page.java:958)
  at org.icepdf.ri.common.views.annotations.AnnotationState.synchronizeState(AnnotationState.java:113)
  at org.icepdf.ri.common.views.annotations.AnnotationState.restore(AnnotationState.java:84)
  at org.icepdf.ri.common.views.annotations.AnnotationState.apply(AnnotationState.java:67)
  at org.icepdf.ri.common.SwingController.propertyChange(SwingController.java:4708)
  at java.beans.PropertyChangeSupport.fire(PropertyChangeSupport.java:335)
  at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:327)
  at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:263)
  at org.icepdf.ri.common.views.DocumentViewControllerImpl.firePropertyChange(DocumentViewControllerImpl.java:1227)
  at org.icepdf.ri.common.views.annotations.AbstractAnnotationComponent.mouseReleased(AbstractAnnotationComponent.java:619)
  at java.awt.Component.processMouseEvent(Component.java:6516)
  at javax.swing.JComponent.processMouseEvent(JComponent.java:3320)
  at java.awt.Component.processEvent(Component.java:6281)
  at java.awt.Container.processEvent(Container.java:2229)
  at java.awt.Component.dispatchEventImpl(Component.java:4872)
  at java.awt.Container.dispatchEventImpl(Container.java:2287)
  at java.awt.Component.dispatchEvent(Component.java:4698)
  at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
  at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)
  at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)
  at java.awt.Container.dispatchEventImpl(Container.java:2273)
  at java.awt.Window.dispatchEventImpl(Window.java:2719)
  at java.awt.Component.dispatchEvent(Component.java:4698)
  at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735)
  at java.awt.EventQueue.access$200(EventQueue.java:103)
  at java.awt.EventQueue$3.run(EventQueue.java:694)
  at java.awt.EventQueue$3.run(EventQueue.java:692)
  at java.security.AccessController.doPrivileged(Native Method)
  at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
  at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
  at java.awt.EventQueue$4.run(EventQueue.java:708)
  at java.awt.EventQueue$4.run(EventQueue.java:706)
  at java.security.AccessController.doPrivileged(Native Method)
  at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
  at java.awt.EventQueue.dispatchEvent(EventQueue.java:705)
  at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
  at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
  at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
  at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
  at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
  at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)

It would appear the error is related to the encoder putting a direct object in the page annotation dictionary. This is technically malformed as the specification states that the array of annotations should be indirect references. The entry looks like this,

/Annots [
<</Type /Annot /Subtype /Link /Rect [511.57 27.26 552.48 19.26] /Contents (þÿ h t t p : / /some url d f) /NM (þÿ 0 0 0 1 - 0 0 0 0) /M (D:20090716235813) /Border [0 0 0] /C [] /A <</S /URI /URI (http://some uri)>> /H /I>>
]
Normally it would look something like this
/Annots [ 43 0 R ]
where 43 0 R would be defined as it's own object.
43 0 obj << ... >> endobj

If I adjust for the null pointer which is the result of how a popup lookup has to happen then every thing work OK, even on the save.

Based QA, marking as fixed.