Navigation has now been re-ordered in accordance with http://docs.moodle.org/en/Development:Navigation_2.0_structure.
This has led to several changes in the way in which navigation is generated included API changes, most notably using the
navigation_nodes add method now returns the newly added node rather than the key.
At the same time the global_navigation_tree block has been renamed to navigation and settings_navigation_tree to settings.
Tim Hunt