Another solution to the problem is to manually add them to the project by editing the project file. To do this right click on your project and select unload. Then right click on the unloaded project and select edit YourProject.csproj. You should see a section that looks like the following:
<Content Include="app.css" />
<Content Include="index.html" />
<Content Include="web.config" />
<TypeScriptCompile Include="app.ts" />
We are going to add lines to one of the item groups to manually include our .js files. The result will look something like:
<Content Include=”*.js” />
If you can include as many lines and wildcards as needed depending on how how your application is structured. Now right click and reload your project, build, and publish to Azure again!