This is how I have my taxonomy setup:
register_taxonomy( 'interest-filter', 'page', array( 'hierarchical' => true, 'labels' => $labels, 'query_var' => true, 'rewrite' => true ) );
And I don’t see a meta box on the edit post page to set the order of the terms. I guess it would be difficult to order something that appears in multiple terms, but your plugin doesn’t mention that it is limited to non-hierarchical taxonomies. Is it?
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