With 2.8 its easy to register custom taxonomies in functions.php and the UI elements auto-generate perfectly in the admin.
However the rewrite rules (and hence taxonomy templates) don't work for your new taxonomies until you either call
$wp_rewrite->flush_rules(); from a plugin registration or happen to visit the permalink settings page in the admin. Registering a new taxonomy doesn't automatically flush the rewrite rules.
What's best practice in theme development for handling this issue?