WordPress will not automatically convert shortcodes that are placed directly in template files.
However, you can take advantage of the do_shortcode(); function to get around this limitation.
e.g. instead of this shortcode
[codewp][mbb_widget id=”MBBv3_SearchForm”][/codewp]
use this PHP code
[codenone]<?php echo do_shortcode(‘[mbb_widget id=”MBBv3_SearchForm”]’); ?>[/codenone]