Every menu item is created with a path (File > Save). The functions are stored in a hash from (menu item path -> action) on the window. When an AtomMenuItem is selected, it looks up the action on the current window based on its path.
This method removes any AtomMenuItems that aren't marked as 'global'. It ignores menu items that aren't instances of our custom subclass. This is needed by specs to clear any menu items added during tests. It will also be needed when a window loses focus and we want to remove any non-global menus associated with the window.