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Through the clone function in Softaculous, I cloned a WP installation to a brand new domain. First thing, I deleted all posts, pages, media, etc. then I created a few new pages, generated a sitemap with All in One SEO, checked it, and submitted it to Google Webmaster Tools. To my surprise, there are 3 crawl errors, pointing to pages of the old site.

I looked everywhere but I can't understand where Google got those links! Where can they hide?

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You need to check Webmaster Tools and click 'LINKED FROM' then delete those references. – Simon Hayter Mar 28 '14 at 11:12
up vote 1 down vote accepted

There might be better ways to do this but when stuck, my default tool is Sublime Text.

Download all site files, download the database, then use ST to do a find (or find and replace) for the old domain (and/or IP address). Be careful though, WordPress uses serialized strings.

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