you will need to convert your folder to an application . To do so, just right click on it, and select "convert to application" After that, as you're publishing a .netCore application, you will have to configure the application pool running that app, and set "Framework version" to unmaged. (and leave the pipeline to integrated)
more information on hosting .NetCore on IIS
This is a one step configuration. All you next publish should work fine.
Some more explanations :
.NetCore is platform agnostics, so it can't know you're deploying on IIS. When you deploy with legacy .net (4.xx) Visual studio has an IIS target for deployment, and did all the work. With .net core, as it can also be run under linux, mac, etc.. the IIS specificities have been removed.
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