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Modified .csproj file for when you need to add bundled scripts that are not included in your project file to the MSDeploy package.
<?xml version="1.0" encoding="utf-8"?>
<Project ToolsVersion="15.0" DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
...
<PropertyGroup>
<CopyAllFilesToSingleFolderForMSDeployDependsOn>
CustomCollectFiles;
$(CopyAllFilesToSingleFolderForMSDeployDependsOn);
</CopyAllFilesToSingleFolderForMSDeployDependsOn>
</PropertyGroup>
<Target Name="CustomCollectFiles">
<ItemGroup>
<_CustomFiles Include="Scripts\your-app-bundle.*" />
<FilesForPackagingFromProject Include="%(_CustomFiles.Identity)">
<DestinationRelativePath>Scripts\%(Filename)%(Extension)</DestinationRelativePath>
</FilesForPackagingFromProject>
</ItemGroup>
</Target>
</Project>
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