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.
Google webmaster tools reporting entire nil subdomain linking to www domain, despite permanent redirect
seo;google search console;subdomain;duplicate content
Have you set up preferred domain in Google Webmaster Tools?