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This warning appear when the Visual Studio project was not built before packaging using NuGet. Just rebuild your project and repack.

1. Go to Build then Rebuild.
2. From command prompt: nuget pack your-project.csproj.

Then it should work.

Note this behavior was filed as an issue in CodePlex.

Note: as per Boris Callens’ response below, can use the -Build to have NuGet do the build