chore: migrate to new kubebuilder project structure

[ChunyiLyu]

Context

If you generate a new kubebuilder project you get a different structure from what we have. For example, controllers/ will locate under internals/controllers. In the future when we need to generate new controllers and webhooks, we do not want to keep using an older kubebuilder to scaffold because we haven't migrated to a new structure. This chore is about bringing kratix repo aligned with the latest structure, we can rely on newer version of kubebuilder.