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I have created custom taxonomy in functions.php and set public=> false and when I try to open taxonomy link in front of web site (mysite.com/custom-taxonomy/test) it doesn't work, it shows 404 page and that is great because I need that to work like that. Problems start when I install SEo plugin (I tried Ultimate SEO and Yoast WordPress SEO). Then my custom taxonomy which I set public false becomes visible on front of the web site. Does anybody know how to solve that problem?

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I don't think setting public to false affects whether or not the archive shows. Rather it is possible you are getting a 404 because your permalinks need updating. It's also possible that the SEO plugins update permalinks for you, which is why it starts working. –  vancoder Apr 4 '13 at 20:49
@vancoder - I need taxonomy to use only in drop downs, not to be accessible over url. Is that possible? –  CroiOS Apr 4 '13 at 21:05
dropdowns where? –  vancoder Apr 4 '13 at 21:21
@vancoder - in front end –  CroiOS Apr 5 '13 at 3:37

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