Align make manifest with controller-manager role

[kerthcet]

Once we run make manifest to generate the kustomized configurations, the controller manager role.yaml will be updated, some verbs will be removed. This is because it's not aligned with the kubebuilder Tag.

I have to add the roles manually to avoid removing some configurations by accident. We should make them aligned and always use make manifest to generate the configurations.

[Jeffwan]

We can come up a better way to do it. The last change is due to standalone component support so we change the folder structure a little bit. Do you think there's a better way? feel free to share your thoughts