in the new asp.net 5 template there's a project.json in which you can exclude certain directories.
Looking at the state of asp.net 5 with visual studio 2015 I can only say that they made it much more difficult and inconvenient to work with task runners like gulp or grunt. Since I'm using Web API 2 to manage my data I switched to Visual Studio Code with bower, gulp and browsersync and this has proven a to be LOT easier and faster with much less clutter.
To make a startup template: https://github.com/Swiip/generator-gulp-angular
Now you can use any editor and you get a clear separation of front end and back end development. Plus you get to know gulp and bower and the (minimal) command line stuff which VS2015 tries to do for you (and fails to do so many times).
Oh yes: you don't have to exclude folders anymore, since the template has a much more sensible folder structure