When duplicating a template page via the page manager (a logical way of creating a new page from within the sitecake interface), sitecake overwrites the HTML in any menu with the sc-nav class. This breaks my menu as I use bootstrap dropdowns for submenus, and sitecake just overwrites all of that, erasing any classes on li elements as well as any submenus.
I am working around this by setting the php file which contains my menu to be read-only on my site. This allows the creation of new pages via the page manager, but with the drawback that newly created pages CANNOT be deleted from within the page manager. The Publish button just keeps spinning and nothing happens.
PLEASE STOP SITECAKE FROM REFORMATTING THE SC-NAV MENU. When I removed the sc-nav class from my menu, obviously this no longer happened, but then only pages in the root folder were displayed in the page manager, and not pages within subdirectories.