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I would like to who the categories of custom post types in the wordpress back-end drag-and-drop menu builder. Is there a filter that I could use to add extra bits of markup there? My idea is to add custom data attributes with category names and put them out as a tooltip with Jquery.

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Probably. Please be more specific. Check the source for the back-end page, look for filters and follow the functions so you can look for filters there too. You are asking people here to do a lot of research on your behalf. –  s_ha_dum Feb 28 '14 at 15:14

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