Primary term

<?php
/*
* Plugin Name:       Permalink Manager - Primary Category
* Plugin URI:        http://maciejbis.net/
* Description:       Plugin that allows to keep select primary categories for posts
* Version:           1.0.0
* Author:            Maciej Bis
* Author URI:        http://maciejbis.net/
* License:           GPL-2.0+
* License URI:       http://www.gnu.org/licenses/gpl-2.0.txt
* Domain Path:       /languages
*/

/**
 * Set primary term
 */
function bis_primary_term($replacement, $replacement_term, $post, $terms, $taxonomy) {
    $bis_primary_terms = get_post_meta($post->ID, 'bis_primary_terms', true);

    // Change primary term if selected for specific post
    if(!empty($bis_primary_terms[$taxonomy])) {
        $replacement_term_id = (int) $bis_primary_terms[$taxonomy];
        $replacement_term = get_term($replacement_term_id, $taxonomy);

        $replacement = Permalink_Manager_Helper_Functions::get_term_full_slug($replacement_term, $terms, 2, null);
    }

    return $replacement;
}
add_filter('permalink_manager_filter_term_slug', 'bis_primary_term', 9, 5);

/**
 * Define custom metaboxes
 */
function bis_add_metaboxes() {
    if(!class_exists('Permalink_Manager_Helper_Functions')) { return; }

    $post_types = get_post_types( array('public' => true) );

  add_meta_box(
    'bis_primary_term',
    __( 'Primary terms', 'bis' ),
    'bis_primary_term_metabox',
    $post_types,
    'side',
    'high'
  );
}
add_action('add_meta_boxes', 'bis_add_metaboxes');

function bis_primary_term_metabox($post) {
    wp_nonce_field( '_bis_metabox_nonce', 'bis_metabox_nonce' );

    // Get all available taxonomies
    $taxonomies = get_object_taxonomies($post, 'objects');
    $bis_primary_terms = get_post_meta(get_the_ID(), 'bis_primary_terms', true);

    foreach($taxonomies as $taxonomy) {
        // Get terms selected for the post
        $terms = get_the_terms($post, $taxonomy->name);

        // If there are no terms selected do not display the field
        if(empty($terms)) { continue; }
    ?>
    <p>
        <label for="bis_primary_terms"><?php echo $taxonomy->label; ?></label>
        <select class="widefat" name="bis_primary_terms[<?php echo $taxonomy->name; ?>]">
            <option>---</option>
            <?php
            foreach($terms as $term) {
                $selected = selected($term->term_id, $bis_primary_terms[$taxonomy->name], false);
                echo "<option value=\"{$term->term_id}\" {$selected}>{$term->name}</option>";
            }
            ?>
        </select>
    </p>
    <?php
    }
}

/**
 * Save custom fields data inside metaboxes
 */
function bis_metaboxes_save( $post_id ) {
    if ( defined( 'DOING_AUTOSAVE' ) && DOING_AUTOSAVE ) return;
    if ( ! isset( $_POST['bis_metabox_nonce'] ) || ! wp_verify_nonce( $_POST['bis_metabox_nonce'], '_bis_metabox_nonce' ) ) return;
    if ( ! current_user_can( 'edit_post', $post_id ) ) return;

    if ( isset( $_POST['bis_primary_terms'] ) ) {
        update_post_meta( $post_id, 'bis_primary_terms', $_POST['bis_primary_terms'] );
    }

}
add_action('save_post', 'bis_metaboxes_save');