Bug 125272 [Viewers] AbstractTreeViewer needs remove(Object parentElement, Object[] childElements)
There is an add(Object parentElement, Object[] childElements) but no corresponding remove(). Without this method, if you have an element that appears under multiple parents, the only way to get model and viewer in sync after removing the element from just one of its parents is calling refresh().
bundles/org.eclipse.jface/src/org/eclipse/jface/viewers/AbstractTreeViewer.java
/**
     * Constant indicating that all levels of the tree should be expanded or
     * collapsed.
     * 
     * @see #expandToLevel
     * @see #collapseToLevel
     */
    public static final int ALL_LEVELS = -1;
    /**
     * List of registered tree listeners (element type: <code>TreeListener</code>). */
    private ListenerList treeListeners = new ListenerList();
    /**
     * The level to which the tree is automatically expanded each time the
     * viewer's input is changed (that is, by <code>setInput</code>). A
     * value of 0 means that auto-expand is off.
     * 
     * @see #setAutoExpandLevel
     */
    private int expandToLevel = 0;
    /**
     * Safe runnable used to update an item.
     */
    class UpdateItemSafeRunnable extends SafeRunnable {