Modified .csproj file for when you need to add bundled scripts that are not included in your project file to the MSDeploy package.

sample-app.csproj

<?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>