flux migrate logic to ssa/manager_apply

[szihai]

In flux migrate, there is a specific piece of logic handling the storageVersion change from v2beta1 to v2.
https://github.com/fluxcd/flux2/blob/main/cmd/flux/migrate.go#L288C1-L318C2
If users forget to run migrate before upgrade, it could cause catastrophic problems combined with "-f" when upgrading. i.e removing all the crds and helmreleases.
Since this is a special version upgrade, why not moving the logic to https://github.com/fluxcd/pkg/blob/main/ssa/manager_apply.go#L256C27-L256C41
This will make sure the upgrade at least will not delete everything because of the version mismatch in crd.