The new controller-gen version only generates CRDs for the first specified path.

An example:

• Checkout https://github.com/kubernetes-sigs/cluster-api
• Run controller-gen:

controller-gen-v0.9.0 \
                paths=./api/... \
                paths=./exp/api/... \
                crd:crdVersions=v1 \
                output:crd:dir=./config/crd/bases

Only CRDs from the ./api/ folder are generated/updated none of ./exp/api/... (i.e. the MachinePool CRD).

I took a closer look at the code and it looks like the metav1Pkg does not match when checking if MachinePool has ObjectMeta and TypeMeta:

Not sure if it would be a correct fix, but by changing the line to

			if fieldPkg != nil && fieldPkg.PkgPath != metav1Pkg.PkgPath {

controller-gen was updating the MachinePool CRD again.

I think it's an additional issue, but after introducing this fix controller-gen did update the MachinePool CRD but it ignored the +kubebuilder:validation:MinLength=1 annotation (i.e. it didn't include minLength in the CRD anymore).