By default in Windows Server 2008 when you are using the Web Management Service (WMSVC) and Web Deploy (also known as MSDeploy) it will use Basic authentication to perform your deployments. If you want to enable Windows Authentication you will need to
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Read the complete post at http://blogs.iis.net/carlosag/archive/2011/12/13/using-windows-authentication-with-web-deploy-and-wmsvc.aspx