The "Web" site is simply the new project you created or existing project you selected when adding a WebRole to your cloud project. So the WebRole's default site (Web) is directly mapped to that web project.
This simply means it will use the assembly of that project for the RoleEntryPoint (WebRole.cs). That's why the output of that project is used in the approot (this is where the RoleEntryPoint is executed) and in the sitesroot (the IIS website).
Now if you want to keep your package small, you can indeed create a dummy site that serves only for the WebRole.cs part, and have a real site besides that. This will create 3 'folders' when deploying to Azure:
- approot => Very small directory containing the dummy site
- sitesroot => Very small directory containing the dummy site
- sitesroot1 => Your real site
What you'll want to do is play with the endpoints to make sure that the dummy site is not exposed by giving it an internal endpoint:
<WebRole name="MyWebRole" vmsize="Small">
<Sites>
<Site name="Web">
<Bindings>
<Binding name="Endpoint1" endpointName="DummyEndpoint" />
</Bindings>
</Site>
<Site name="RealWebApplication" physicalDirectory="..MvcApplication1">
<Bindings>
<Binding name="Endpoint2" endpointName="RealEndpoint" />
</Bindings>
</Site>
</Sites>
<Endpoints>
<InputEndpoint name="RealEndpoint" protocol="http" port="80" />
<InternalEndpoint name="DummyEndpoint" protocol="http" />
</Endpoints>
...
</WebRole>
And your dummy web application will look like this:
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