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The problem is that the NuGet packages I am deploying do not provide Runtime assemblies and therefore the applications that are built against these NuGet packages do not provide the "runtime" node and therefore the loader does not know how to locate the assemblies.

To solve this problem I have created a repository that implements an application that adds the "runtime" node with the assembly name to the .deps.json file of the compiled application.
This application can be added as a Post Build Event in the NuGet package.

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Answer selected by joseangelmt
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