For making WebSetup with .NET 2.0, one need to download webdeployment.msi file from microsoft website. Advantage of webdeployment is, it copies only the design file not the code behind file. If you try to create the web setup without the webdeployment project added code behind file will also go in the setup.
Visual Studio 2005 Web Deployment Projects provide additional functionality to build and deploy Web sites and Web applications in ASP.NET 2.0 and Visual Studio 2005. This add-in includes a tool to merge the assemblies created during ASP.NET 2.0 pre-compilation, and provides a comprehensive UI within Visual Studio 2005 to manage build configurations, merging, and using pre-build and post-build tasks with MSBuild.
For more details about creating the Web Setup using web deployment project take a look at this link.
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