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Registers a menu location to use with navigation menus. Even if you explicitly set theme support for navigation menus, this function must be in your theme's functions file for WordPress to recognize navigation menu support in your theme.
<?php register_nav_menu( 'your-menu-handle', 'Your Menu Label' ); ?>
This is the code you need in your functions.php to enable native navigation menu support:
register_nav_menu('main', 'Main navigation menu');