Custom Post type and permalink settings

You can use the rewrite parameter to disable the front portion of the URLs (/academy/ in your case) for custom post types.

function create_posttypes() {
    $labels1 = array(
            'name' => __( 'Definitions' ),
            'singular_name' => __( 'Definition' ),
            'all_items' => __( 'All Definitions' ),
            'view_item' => __( 'View Definition' ),
            'add_new_item' => __( 'Add New Definition' ),
            'edit_item' => __( 'Edit Definition' ),
            'update_item' => __( 'Update Definition' ),
            'search_items' => __( 'Search Definitions' ),
            'not_found' => __( 'Not Found' ),
            'not_found_in_trash' => __( 'Not Found in Trash' ),
        );
    $args1 = array(
            'label' => 'Definitions',
            'description' => 'Definitions received',
            'labels' => $labels1,
            'public' => true,
            'has_archive' => true,
            'rewrite' => array(
                'slug' => 'glossary',
                'with_front' => false,
             ),
            'hierarchical' => false,
            'show_ui' => true,
            'show_in_menu' => true,
            'show_in_nav_menus' => true,
            'show_in_admin_bar' => true,
            'menu_position' => 5,
            'can_export' => true,
            'exclude_from_search' => false,
            'publicly_queryable' => true,
            'capability_type' => 'page',
            'supports' => array('title','thumbnail', 'revisions', 'page-attributes')
        );
    register_post_type( 'definitions', $args1 );
}