The answer is here:
http://sharepoint.mindsharpblogs.com/Ben/archive/2009/10/29/SharePoint-Server-2010-Site-Directory-%28where-did-it-go%5Bques%5D%29.aspx

The template is still there but hidden and the Site Directory links scan still forms a part of Central Administration, you will just have to set up a sub-site to act as your site directory by hand. Remember to activate the Publishing feature if you did not use a Publishing template for the site collection.

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