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My problem is two fold:

  1. After migrating my site, many of the URLs aren't working, and producing 404 errors. But the main landing page is working, and so are most/all of the features on the main page.

  2. My configuration for custom 404 error pages are being ignored, and were working before copying the root of the web server files over. This I'm not so worried about.

These are the steps I used to migrate the site:

  1. mysqldump the database from the originating server.
  2. Import the database to the new server, using the same mysql credentials.
  3. Copy the root of the web server files over to the new location.

This is my setup: CentOS6 nginx MySQL php, php-fpm Drupal 7

The only real difference between the originating server and the target server is that the originating server is centos5.

I am not a drupal expert, but I did some searching and I keep coming across "clean urls". I'm not exactly sure what that is.

Is there a better way to migrate a drupal site, or is there something I did wrong?

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This indeed sounds like a clean URL problem.

Standard Drupal URLs use query strings like: www.example.com/?q=string/string/site Clean URLs rewrite this to www.example.com/string/string/site which is better for SEO.

Check the browser's adress bar to see if clean URLs are working. If not and if you used them on the previous install, you need to either deactivate them in drupal or get them working again. You need to activate it in settings and use correct .htaccess with Clean URLs rewrite rule.

The reason why the home page is working is that there is no query string in www.example.com/

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I'm sure there are different ways to do this, but I've been successful using the Backup and Migrate project. Follow the directions in this great article: http://www.seascapewebdesign.com/blog/how-transfer-your-website-one-server-another

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