Now only a single AnnotationManager instance is created even when multiple documents are loaded. This means if you previously added AnnotationManager event handlers inside the documentLoaded event you should move them to the viewerLoaded event otherwise you'll receive an extra event for every new document you load.
All old annotation popup behavior (notes that appeared directly on the document, NOT in the notes panel) has been removed
The enableAnnotations option is now set to true by default. If you want annotations to be disabled you should explicitly set this to false.