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I Backed up my site then totally re-did my server with a different Control Panel which created a different directory structure /var/www/vhosts/user/ I put the files into the httpdocs folder and put the database back correctly (I think) I can see the main page but clicking on any links gets me a Not Found Message I have tried running update.php and I cannot access /user/login either.

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Can you give us a link to your site so we can check it out? – d-_-b Jun 3 '10 at 0:40

Looks like your apache doesn't have mod_rewrite enabled, which is needed to have clean urls enabled in Drupal. Make sure to enable that... in Ubuntu a2enmod rewrite will do the trick.

Try going to ?q=user/login and see if that allows you to login to your site.

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