Question: The title should be self-explanitory, but just in case. I am trying to build an angular application which will be hosted on azure. Currently I am having some issues with using kestrel, so I would like to build the application in visual studio but without using any .net code (so no startup.cs or program.cs).
If the answer is plainly no, then I guess I will need to find another IDE that will do what I require.

Answer: 
Yes it is very much possible with visual studio to develop a SPA in angular without using .net framework. Below are the steps you can follow to getting started with a SPA in angular using visual studio.

Goto: **File > New > Project**

From the below screen selecet **ASP.NET Web Application**[![enter image description here](https://i.stack.imgur.com/WpcZG.jpg)](https://i.stack.imgur.com/WpcZG.jpg)

Provide Name, Location, Solution click **OK** will get the below popup[![enter image description here](https://i.stack.imgur.com/njaKv.jpg)](https://i.stack.imgur.com/njaKv.jpg)

From the above Popup select Empty and Press OK to create your project.
Now add an html file say **index.html** to the project. Write the below code in index.html

```html
<head>
    <title></title>
    <script src="https://cdnjs.cloudflare.com/ajax/libs/angular.js/1.6.1/angular.min.js"></script>
</head>
<body>
    <div ng-app>
        Message:<input type="text" ng-model="message" />
        <hr>
        <div>Entered Message:{{message}}</div>
    </div>
</body>
</html>
```

And you are good to go. Right click on `index.html` and select `View In Browser` you will see the output in your browser something like this.

[![enter image description here](https://i.stack.imgur.com/w30JR.jpg)](https://i.stack.imgur.com/w30JR.jpg) 

Now You can can create a directory structure accordingly. Below are few link that can help you with the directory structure.

[Directory Structure Angular](https://scotch.io/tutorials/angularjs-best-practices-directory-structure)

[Angular Folder Structure](https://stackoverflow.com/questions/18542353/angularjs-folder-structure)

[Angular App Structure Guideliines](https://johnpapa.net/angular-app-structuring-guidelines/)

Or you can follow the steps as stated on official Angular website for getting started with an angular project in Visual Studio 

[VISUAL STUDIO 2015 QUICKSTART ANGULAR](https://angular.io/docs/ts/latest/cookbook/visual-studio-2015.html)

Hope this Helps :)
If you using node toolings to build you project you may want to try [Node.js Tools for Visual Studio](https://www.visualstudio.com/vs/node-js/)

It does have support for gulp/grunt tasks as well as it has integration with azure. The support is provided via custom project types.