Add category base to url in custom post type/taxonomy

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I am building an LMS type system in WordPress, controlled by Custom Post types.
The post type is called Lessons (with a slug of courses) and it has one custom taxonomy (category) called courses.

The domain url structure shows right now as:

domain.com/courses/lesson-name.

I want it to become:

domain.com/courses/[course-name{category}]/lesson-name

or essentially:

/[cpt]/%category%/%postname%/

here is the plugin I wrote that is controlling the CPTs now.

function rflms_post_type() {
    $labels = array(
        'name'                => _x( 'Lessons', 'Post Type General Name', 'text_domain' ),
        'singular_name'       => _x( 'Lesson', 'Post Type Singular Name', 'text_domain' ),
        'menu_name'           => __( 'Lessons', 'text_domain' ),
        'parent_item_colon'   => __( 'Parent Product:', 'text_domain' ),
        'all_items'           => __( 'All Lessons', 'text_domain' ),
        'view_item'           => __( 'View Lesson', 'text_domain' ),
        'add_new_item'        => __( 'Add New Lesson', 'text_domain' ),
        'add_new'             => __( 'New Lesson', 'text_domain' ),
        'edit_item'           => __( 'Edit Lesson', 'text_domain' ),
        'update_item'         => __( 'Update Lesson', 'text_domain' ),
        'search_items'        => __( 'Search Lessions', 'text_domain' ),
        'not_found'           => __( 'No Lessons Found', 'text_domain' ),
        'not_found_in_trash'  => __( 'No Lessons Found in Trash', 'text_domain' ),
    );

    $args = array(
        'label'               => __( 'Lessons', 'text_domain' ),
        'description'         => __( 'Referable Lessons', 'text_domain' ),
        'labels'              => $labels,
        'hierarchical'        => false,
        'public'              => true,
        'show_ui'             => true,
        'show_in_menu'        => true,
        'show_in_nav_menus'   => true,
        'show_in_admin_bar'   => true,
        'supports'        => array('premise-member-access', 'title', 'editor', 'author', 'thumbnail', 'excerpt', 'comments'),
        'menu_position'       => 5,
        'menu_icon'           => null,
        'can_export'          => true,
        'has_archive'         => true,
        'exclude_from_search' => false,
        'publicly_queryable'  => true,
        'capability_type'     => 'post',
        'rewrite'                    => array('slug' => 'courses'),
    );

    register_post_type( 'lessons', $args );


// Hook into the 'init' action

}
add_action( 'init', 'rflms_post_type', 0 );

// Register Custom Taxonomy
function custom_taxonomy()  {
    $labels = array(
        'name'                       => _x( 'Courses', 'Taxonomy General Name', 'text_domain' ),
        'singular_name'              => _x( 'Course', 'Taxonomy Singular Name', 'text_domain' ),
        'menu_name'                  => __( 'Courses', 'text_domain' ),
        'all_items'                  => __( 'All Courses', 'text_domain' ),
        'parent_item'                => __( 'Parent Course', 'text_domain' ),
        'parent_item_colon'          => __( 'Parent Course:', 'text_domain' ),
        'new_item_name'              => __( 'New Course Name', 'text_domain' ),
        'add_new_item'               => __( 'Add New Course', 'text_domain' ),
        'edit_item'                  => __( 'Edit Course', 'text_domain' ),
        'update_item'                => __( 'Update Course', 'text_domain' ),
        'separate_items_with_commas' => __( 'Separate Courses with commas', 'text_domain' ),
        'search_items'               => __( 'Search Courses', 'text_domain' ),
        'add_or_remove_items'        => __( 'Add or Remove Courses', 'text_domain' ),
        'choose_from_most_used'      => __( 'Choose from Most Used courses', 'text_domain' ),
    );

    $args = array(
        'labels'                     => $labels,
        'hierarchical'               => true,
        'public'                     => true,
        'show_ui'                    => true,
        'show_admin_column'          => true,
        'show_in_nav_menus'          => true,
        'show_tagcloud'              => false,
        'rewrite'                    => array('slug' => 'courses'),
    );

    register_taxonomy( 'course', 'lessons', $args );
}

// Hook into the 'init' action
add_action( 'init', 'custom_taxonomy', 0 );

9

Change your rewrite to add the course query var:

'rewrite' => array('slug' => 'courses/%course%')

Then filter post_type_link to insert the selected course into the permalink:

function wpa_course_post_link( $post_link, $id = 0 ){
    $post = get_post($id);  
    if ( is_object( $post ) ){
        $terms = wp_get_object_terms( $post->ID, 'course' );
        if( $terms ){
            return str_replace( '%course%' , $terms[0]->slug , $post_link );
        }
    }
    return $post_link;  
}
add_filter( 'post_type_link', 'wpa_course_post_link', 1, 3 );

There are also plugins like Custom Post Type Permalinks that can do this for you.

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