Last month, Tim Heuer blogged about an issue in Visual Web Developer 2005 / VS 2005 in that Intellisense stops working for the Web.config file after using the ASP.NET Web Site Administration Tool (WSAT).  This is purely an Intellisense issue as the ASP.NET application will still run normally.

Here's the workaround:
Just remove the xmlns attribute (which was added by WSAT) of the Web.config <configuration> node to get Intellisense back.

Scott Guthrie has a post on this workaround too.

This Intellisense issue is also being tracked at MSDN Product Feedback Center.

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