Ionic 2 is currently in beta, which means that things may change and break between the releases (and in fact there are a lot of changes with a few breaking from time to time).
I would recommend you after every update to a newer release of Ionic 2 to create a new blank project (ionic start Test blank --v2, if you use TypeScript add also --ts) and copy the config files from there (or even better - perform a merge if you’ve made changes to them).
Alternatively check the latest config files in the ionic2-app-base repo (when using TypeScript, make sure to check the typescript branch) and update your config files accordingly.