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I am struggling to understand the concepts around Azure Resource Manager. When I create an Azure Resource Manager project in a solution with existing Azure Web Apps and other artifacts, how can I say that my new Resource Group should include those projects and how can I specify the publish settings so that deployment of the ARM project publishes those websites too.

My feeling is that I am not really getting the conceptual model behind this stuff at the moment.

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UPDATE: while the below is basically correct, now it is possible to do simply by adding a project reference to the web app. The zip file appears in a subfolder.

OK I got the answer I needed to this. For web apps, the ARM project needs to include a Web Deploy for Web Apps resource, and it needs to point to a package. The publish method for the web app needs to be set to 'package'. Detailed instructions on this excellent blog post: http://blogs.technet.com/b/georgewallace/archive/2015/05/10/deploying-a-website-with-content-through-visual-studio-with-resource-groups.aspx