This looks cool. I've never used webpack, but this seems like a good place to start.
I'm a bit confused about the choice of package inclusions though. Waypoints.js and scrollTo.js both feel like pretty opinionated choices. That is, it seems like you have a particular idea in mind for the UI based on the inclusion of those packages, but the UI is empty.
I think the inclusion of a (not overly complex) UI that makes interesting use of the packages you included would help this project get a lot of traction, in that it would more viscerally demonstrate that the user can go from nothing to a pretty decent website in ~10 seconds.