Theme Convert PHP code to shortcode

This should do it, I used output buffering with ob_start() and ob_get_clean:

<?php

/**
 * Breadcrumbs based on theme's functions
 *
 * @author  Nabil Kadimi <[email protected]>
 * @link    http://wordpress.stackexchange.com/a/242547/17187
 */
add_action( 'init', function() {
    add_shortcode( 'mycrumbs', function() {

        /**
         * Start capturing output.
         */
        ob_start();

        ?>
        <div class="x-breadcrumb-wrap">
            <div class="x-container max width">
                <?php x_breadcrumbs(); ?>
                <?php if ( is_single() || x_is_portfolio_item() ) : ?>
                    <?php x_entry_navigation(); ?>
                <?php endif; ?>
            </div>
        </div>
        <?

        /**
         * Stop capturing output and return what was captured to WordPress.
         */
        return ob_get_clean();

    } ); // add_shortcode( 'mycrumbs', closure );
} ); // add_action( 'init', closure );