WordPress 4.0 appears to have altered the way the main navigation menu is retrieved. Previously, themes would use:
wp_nav_menu();
where they needed the main menu to appear. With WordPress 4.0, this behavior has been altered. Instead you will need to use:
wp_nav_menu(array('theme_location'=>'primary'));
Without indicating that you need to use the “Primary” menu, wp_nav_menu() will fall back to wp_page_menu().
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