Decide a migration path for deprecated certManagerVersionAnnotation

### What steps did you take and what happened?

We have a [`certManagerVersionAnnotation = "certmanager.clusterctl.cluster.x-k8s.io/version`](https://github.com/kubernetes-sigs/cluster-api/blob/main/cmd/clusterctl/client/cluster/cert_manager.go#L46-L51) annotation which is maintained only for supporting upgrades from clusters created with clusterctl v1alpha3. We are working towards removing a previously deprecated code in https://github.com/kubernetes-sigs/cluster-api/pull/9136 and this annotation might not be removed since there is no migration code for it and we have to keep it in order to support clusters created with this annotation.

### What did you expect to happen?

We need to decide how we would provide a clear migration tasks for this specific annotation not to break clusters created with v1alpha3

### Cluster API version

main

### Kubernetes version

N/A

### Anything else you would like to add?

See more the discussion here: https://github.com/kubernetes-sigs/cluster-api/pull/9136#discussion_r1286060493

### Label(s) to be applied

/kind bug
/area clusterctl

Start with cmd/clusterctl/client/cluster/cert_manager.go and the discussion in pull request #9136. Determine how clusters created with clusterctl v1alpha3 use certManagerVersionAnnotation and document a migration path that preserves compatibility. Done means the migration tasks and removal conditions are agreed and recorded.

Written by the indexing model from the issue text.