`bases` is a deprecated section of the kustomize API, and is replaced by
`resources` in v2.1.0 onwards. Since we use kustomize 3.X, this moves
our kustomization yamls to the new accepted format.

This also moves our Makefile away from using `kubectl <apply/delete>
-k`, which uses kubectl's older, bundled version of Kustomize v2.0.3
(see [this issue](https://github.com/kubernetes/kubectl/issues/818)).