You can change your project XML to add existing subfolders and structures automatically into your project like "node_modules" from NPM:
This is for older MSBuild / Visual Studio versions
<ItemGroup>
<Item Include="$([System.IO.Directory]::GetFiles("$(MSBuildProjectDirectory)\node_modules","*",SearchOption.AllDirectories))"></Item>
</ItemGroup>
For the current MSBuild / Visual Studio versions:
Just put it in the nodes of the xml:
<Project>
</Project>
In this case just change $(MSBuildProjectDirectory)\node_modules to your folder name.