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Looking in webmaster tools it is reported that I have a thousand of so inbound links from my root domain, domain.com, to www.domain.com. This is despite the fact I have a permanent redirect setup in nginx's conf file to www.

Obviously I don't want to be penalised for cross domain linking but how can I clear this mess up? To my knowledge the nil domain was never accessible so I don't know how google apparently indexed it.

Are there some particular steps I should take to resolve this? Is it likely that I am being penalised for duplicate content.

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Have you set up preferred domain in Google Webmaster Tools?

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Well, the answer to that is 'kind of'. I needed moved the site to a new domain near the end of its development so set up a change of address request. The previous site was on a www subdomain and I requested the move to the new www. I am informed that due to this request that defining a preferred subdomain is not available to me. All in all it's a mess and given the site on the old domain had no particular ranking anyway I'm going to remove the request, set up the preferred subdomain and request a site reconsideration, in case I have been penalized. Thanks for your help. –  mark Apr 11 '11 at 19:39

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