Bug 114637 [Preferences] PlatformUI.getPreferenceStore() != WorkbenchPlugin.getPreferenceStore()
Somehow these two preference stores are no longer the same. This is causing all kinds of problems in themes because we're hooking theme listeners to one and then firing changes at another. As a result, themes just aren't working. I'm going to investigate
bundles/org.eclipse.ui.ide/src/org/eclipse/ui/views/navigator/ResourcePatternFilter.java
initializeFromPreferences();
        return this.matchers;
    }
    /**
     * Gets the patterns for the receiver. Returns the cached values if there
     * are any - if not look it up.
     */
    public String[] getPatterns() {
        if (this.patterns == null)
            initializeFromPreferences();
        return this.patterns;
    }
    /**
     * Initializes the filters from the preference store.
     */
    private void initializeFromPreferences() {
        
        IPreferenceStore viewsPrefs = IDEWorkbenchPlugin.getDefault()
                .getPreferenceStore();
        String storedPatterns = viewsPrefs.getString(FILTERS_TAG);
        if (storedPatterns.length() == 0) {
            
            IPreferenceStore workbenchPrefs = PlatformUI.getWorkbench()
                    .getPreferenceStore();
            storedPatterns = workbenchPrefs.getString(FILTERS_TAG);
            if (storedPatterns.length() > 0) {
                viewsPrefs.setValue(FILTERS_TAG, storedPatterns);
                workbenchPrefs.setValue(FILTERS_TAG, ""); 
            }
        }