There is a documentation bug/omission in the JSF 2.0/2.1 JavaDoc. Specifically, the omission is that the Application#getNavigationHandler() method  is supposed to let you specify a wrappable implementation from the <navigation-handler> within the <application> element of faces-config. The feature is formally specified in the faces-config XML Schema . I just checked and both Mojarra  and MyFaces  implement this feature.
Please refer to the Application#getResourceHandler() method  for an example of how to describe this feature in JavaDoc.