Resolve "Upgrade flux to v2.0"

Implements the first part of #1635 (closed) : upgrading flux CRDs and controllers to flux v2.

We also need to change our manifests (Kustomizations, GitRepos, HelmRepos) to the new API versions, but we prefer to do that in a later Stackspin release to make sure we don't run into ordering issues, where the new manifests get processed by the old controllers.