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Using the Visual Studio Integrated UI 

Visual Studio 2005

From inside Visual Studio, you can create and edit Dotfuscator projects and add them to your existing solutions. During a build, a Dotfuscator project can consume binary outputs (i.e. your compiled .NET assemblies) from the development projects in your solution, and in turn, expose the obfuscated outputs to deployment projects. Using the Visual Studio Integrated UI is the easiest way to configure and seamlessly use Dotfuscator. Note: The Visual Studio Integrated UI is not part of the Community Edition. If you are using the Community Edition, we recommend that you download the free trial version of the Professional Edition to experience this seamless configuration first hand.

For details, see the online user's guide.