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I like your new (to v2.x) negative margin trick to change the source order of navigation. I successfully used the same trick to create a Leaderboard region, in source order at the bottom but positioned at the very top.
But how do I add another "featured" region above #content and sidebars? I've tried a few things but each time navigation remains positioned below the "featured" region, which I don't want (otherwise I would just use the existing header region of course).