When I publish under Visual Studio 2015 CTP 5 then I don't have to do setting for application pool CLR version.
Now for ASP.net core application and as per documentation (http://docs.asp.net/en/latest/publishing/iis.html) we have to do setting for application pool clr to No managed code.
Why it is like that ?
ASP.NET Core applications no longer run inside IIS but run out-of-process and IIS acts only as a reverse proxy. This functionality is provided by the AspNetCoreModule which is a native IIS module. Since no managed code runs in the IIS process it is recommended to set application pool as "No managed code". I wrote a detailed blog post describing how ASP.NET Core applications are running with IIS. You can find it here.
This is because ASP.NET Core runs as a plain old command line application outside of the IIS. Therefore, IIS is merely a pass-through to Kestrel, which is the ASP.NET Core web server which runs in it's own separate process. This platform is what provides the cross-platform capabilities of .NET Core.
