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My primary navigation menu consists of pages, categories, and custom taxonomy. It appears to be in a random order. How do I adjust the order of the links? (the drag/drop in wp menus panel doesn't seem to have any effect)

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This may depend on the theme you are using. Recent themes support the selection of primary of main menus and potentially other menus, go to yoursite.com/wp-admin/nav-menus.php and create a menu, then set it as the main menu, in the top left "theme locations" section. If you do not see this section then you need to enable it for your theme.

this gives you full control over hierarchy of your menu, what items are included and the order of the items.

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I have it set as Main Menu under theme locations. So it would appear my theme supports it. (I'm using "Bones" theme if you are familiar. Moving them up and down is not reflected in the order on the front end up the site; though hierarchy is... – Sam Jun 25 '12 at 0:19
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Turns out under my theme (Bones) bottom position is actually the first one to display on front end. I had it backwards.

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