On new WordPress installs, I’ve used the plugin ‘Top Level Categories’ more than a few times, and can certainly recommend it. Just be aware when fiddling with your categories that sometimes it creates weird structures if you set up the individual categories first – the last time I used it I installed the plugin first, then assigned each post a new category. This seemed to solve the problem. I would suggest using the /%category%/%postname%/ permalink structure, and twinned with an SEO plugin controller you’ll have pretty good control over your URL and site structure… best to get it as soon as possible before you make too many pages!
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Removes the prefix from the URL for a category. For instance, if your old category link was