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How do I change the order of taxonomies in the sub menu?

In your header.php file, replace:

$terms = get_terms($primaryTaxonomy->id, array('parent' => 0, 'hide_empty' => 0));

With:

$terms = get_terms($primaryTaxonomy->id, array('parent' => 0, 'hide_empty' => 0, 'orderby' => id));