Update kustomization.yaml files to new format

kustomize has deprecated the older format which our older kustomization files were based on. These older format files were leading to a lot of deprecation warnings from kustomize during our build processes.

We used kustomize edit fix command to update our old kustomize files to our new kustomize files. This PR was largely auto-generated using the following command.

```
$ find . -type d -exec bash -c 'cd {} && kustomize edit fix' \;
```

config/crd/kustomization.yaml

@@ -8,7 +8,6 @@ resources:
 - bases/infrastructure.cluster.x-k8s.io_nutanixclustertemplates.yaml
 #+kubebuilder:scaffold:crdkustomizeresource
 
-patchesStrategicMerge:
 # [WEBHOOK] To enable webhook, uncomment all the sections with [WEBHOOK] prefix.
 # patches here are for enabling the conversion webhook for each CRD
 #- patches/webhook_in_nutanixclusters.yaml
@@ -25,34 +24,38 @@ patchesStrategicMerge:
 #- patches/cainjection_in_nutanixclustertemplates.yaml
 #+kubebuilder:scaffold:crdkustomizecainjectionpatch
 
-patchesJson6902:
   # controller-gen doesn't allow for complex anyOf declarations in CRD generation code markers so we have to add these
   # via a JSON patch instead.
   #
   # This enforces the Prism Central address to be either a hostname or an IP address without resorting to complex
   # regular expressions.
-  - target:
-      group: apiextensions.k8s.io
-      version: v1
-      kind: CustomResourceDefinition
-      name: nutanixclusters.infrastructure.cluster.x-k8s.io
-    patch: |-
-      - op: add
-        path: /spec/versions/0/schema/openAPIV3Schema/properties/spec/properties/prismCentral/properties/address/anyOf
-        value:
-          - format: hostname
-          - format: ipv4
-          - format: ipv6
-      - op: add
-        path: /spec/versions/1/schema/openAPIV3Schema/properties/spec/properties/prismCentral/properties/address/anyOf
-        value:
-          - format: hostname
-          - format: ipv4
-          - format: ipv6
 
 # the following config is for teaching kustomize how to do kustomization for CRDs.
 configurations:
 - kustomizeconfig.yaml
 
-commonLabels:
-  cluster.x-k8s.io/v1beta1: v1beta1
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+labels:
+- includeSelectors: true
+  pairs:
+    cluster.x-k8s.io/v1beta1: v1beta1
+patches:
+- patch: |-
+    - op: add
+      path: /spec/versions/0/schema/openAPIV3Schema/properties/spec/properties/prismCentral/properties/address/anyOf
+      value:
+        - format: hostname
+        - format: ipv4
+        - format: ipv6
+    - op: add
+      path: /spec/versions/1/schema/openAPIV3Schema/properties/spec/properties/prismCentral/properties/address/anyOf
+      value:
+        - format: hostname
+        - format: ipv4
+        - format: ipv6
+  target:
+    group: apiextensions.k8s.io
+    kind: CustomResourceDefinition
+    name: nutanixclusters.infrastructure.cluster.x-k8s.io
+    version: v1

config/default/kustomization.yaml

@@ -9,13 +9,7 @@ namespace: capx-system
 namePrefix: capx-
 
 # Labels to add to all resources and selectors.
-commonLabels:
-  cluster.x-k8s.io/provider: "infrastructure-nutanix"
 
-bases:
-- ../crd
-- ../rbac
-- ../manager
 # [WEBHOOK] To enable webhook, uncomment all the sections with [WEBHOOK] prefix including the one in
 # crd/kustomization.yaml
 #- ../webhook
@@ -24,11 +18,9 @@ bases:
 # [PROMETHEUS] To enable prometheus monitor, uncomment all sections with 'PROMETHEUS'.
 #- ../prometheus
 
-patchesStrategicMerge:
 # Protect the /metrics endpoint by putting it behind auth.
 # If you want your controller-manager to expose the /metrics
 # endpoint w/o any authn/z, please comment the following line.
-- manager_auth_proxy_patch.yaml
 
 # Mount the controller config file for loading manager configurations
 # through a ComponentConfig type
@@ -44,31 +36,15 @@ patchesStrategicMerge:
 #- webhookcainjection_patch.yaml
 
 # the following config is for teaching kustomize how to do var substitution
-vars:
-# [CERTMANAGER] To enable cert-manager, uncomment all sections with 'CERTMANAGER' prefix.
-#- name: CERTIFICATE_NAMESPACE # namespace of the certificate CR
-#  objref:
-#    kind: Certificate
-#    group: cert-manager.io
-#    version: v1
-#    name: serving-cert # this name should match the one in certificate.yaml
-#  fieldref:
-#    fieldpath: metadata.namespace
-#- name: CERTIFICATE_NAME
-#  objref:
-#    kind: Certificate
-#    group: cert-manager.io
-#    version: v1
-#    name: serving-cert # this name should match the one in certificate.yaml
-#- name: SERVICE_NAMESPACE # namespace of the service
-#  objref:
-#    kind: Service
-#    version: v1
-#    name: webhook-service
-#  fieldref:
-#    fieldpath: metadata.namespace
-#- name: SERVICE_NAME
-#  objref:
-#    kind: Service
-#    version: v1
-#    name: webhook-service
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+resources:
+- ../crd
+- ../rbac
+- ../manager
+labels:
+- includeSelectors: true
+  pairs:
+    cluster.x-k8s.io/provider: infrastructure-nutanix
+patches:
+- path: manager_auth_proxy_patch.yaml

config/prometheus/kustomization.yaml

@@ -1,2 +1,4 @@
 resources:
 - monitor.yaml
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization

config/rbac/kustomization.yaml

@@ -1,18 +1,20 @@
-resources:
 # All RBAC will be applied under this service account in
 # the deployment namespace. You may comment out this resource
 # if your manager will use a service account that exists at
 # runtime. Be sure to update RoleBinding and ClusterRoleBinding
 # subjects if changing service account names.
+# Comment the following 4 lines if you want to disable
+# the auth proxy (https://github.com/brancz/kube-rbac-proxy)
+# which protects your /metrics endpoint.
+resources:
 - service_account.yaml
 - role.yaml
 - role_binding.yaml
 - leader_election_role.yaml
 - leader_election_role_binding.yaml
-# Comment the following 4 lines if you want to disable
-# the auth proxy (https://github.com/brancz/kube-rbac-proxy)
-# which protects your /metrics endpoint.
 - auth_proxy_service.yaml
 - auth_proxy_role.yaml
 - auth_proxy_role_binding.yaml
 - auth_proxy_client_clusterrole.yaml
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization

templates/base/kustomization.yaml

@@ -1,19 +1,19 @@
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 
-namespace: "${NAMESPACE}"
+namespace: ${NAMESPACE}
 
-bases:
-  - ../ccm
-  - ./cm.yaml
-  - ./secret.yaml
-  - ./nutanix-cluster.yaml
-  - ./cluster-without-topology.yaml
-  - ./kcp.yaml
-  - ./kct.yaml
-  - ./nmt.yaml
-  - ./md.yaml
-  - ./mhc.yaml
 
-patchesStrategicMerge:
-- ./ccm-patch.yaml
+resources:
+- ../ccm
+- ./cm.yaml
+- ./secret.yaml
+- ./nutanix-cluster.yaml
+- ./cluster-without-topology.yaml
+- ./kcp.yaml
+- ./kct.yaml
+- ./nmt.yaml
+- ./md.yaml
+- ./mhc.yaml
+patches:
+- path: ./ccm-patch.yaml

templates/ccm/kustomization.yaml

@@ -2,11 +2,11 @@ apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 
 configMapGenerator:
-- name: nutanix-ccm
-  behavior: merge
+- behavior: merge
   files:
   - nutanix-ccm.yaml
+  name: nutanix-ccm
 
-bases:
-  - ./nutanix-ccm-crs.yaml
-  - ./nutanix-ccm-secret.yaml
+resources:
+- ./nutanix-ccm-crs.yaml
+- ./nutanix-ccm-secret.yaml

templates/clusterclass/kustomization.yaml

@@ -1,10 +1,10 @@
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 
-bases:
-  - ./nct.yaml
-  - ./clusterclass.yaml
-  - ./nmt-cp.yaml
-  - ./nmt-md.yaml
-  - ./kcpt.yaml
-  - ./kct.yaml
+resources:
+- ./nct.yaml
+- ./clusterclass.yaml
+- ./nmt-cp.yaml
+- ./nmt-md.yaml
+- ./kcpt.yaml
+- ./kct.yaml

templates/csi/kustomization.yaml

@@ -2,17 +2,17 @@ apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 
 configMapGenerator:
-- name: nutanix-csi
-  behavior: merge
+- behavior: merge
   files:
   - nutanix-csi-storage.yaml
   - nutanix-csi-snapshot.yaml
   - nutanix-csi-webhook.yaml
+  name: nutanix-csi
 
 resources:
 - ../base/
 - nutanix-csi.yaml
 - nutanix-csi-crs.yaml
 
-patchesStrategicMerge:
-- csi-patch.yaml
+patches:
+- path: csi-patch.yaml

templates/topology/kustomization.yaml

@@ -2,17 +2,17 @@ apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 
 configMapGenerator:
-- name: nutanix-ccm
-  behavior: merge
+- behavior: merge
   files:
   - nutanix-ccm.yaml
+  name: nutanix-ccm
 
-bases:
-  - ./cm.yaml
-  - ./cluster-with-topology.yaml
-  - ./secret.yaml
-  - ./nutanix-ccm-secret.yaml
-  - ./nutanix-ccm-crs.yaml
 
-patchesStrategicMerge:
-- ./ccm-patch.yaml
+resources:
+- ./cm.yaml
+- ./cluster-with-topology.yaml
+- ./secret.yaml
+- ./nutanix-ccm-secret.yaml
+- ./nutanix-ccm-crs.yaml
+patches:
+- path: ./ccm-patch.yaml

test/e2e/data/infrastructure-nutanix/v1.2.4/cluster-template/kustomization.yaml

@@ -1,14 +1,12 @@
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
-
-bases:
-  - ../base/cluster-with-kcp.yaml
-  - ../base/secret.yaml
-  - ../base/cm.yaml
-  - ../base/nmt.yaml
-  - ../base/md.yaml
-  - ../base/mhc.yaml
-  - ../base/crs.yaml
-
-patchesStrategicMerge:
-  - ../base/cni-patch.yaml
+resources:
+- ../base/cluster-with-kcp.yaml
+- ../base/secret.yaml
+- ../base/cm.yaml
+- ../base/nmt.yaml
+- ../base/md.yaml
+- ../base/mhc.yaml
+- ../base/crs.yaml
+patches:
+- path: ../base/cni-patch.yaml

test/e2e/data/infrastructure-nutanix/v1.3.0/cluster-template/kustomization.yaml

@@ -1,23 +1,20 @@
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
-
 configMapGenerator:
-- name: nutanix-ccm
-  behavior: merge
+- behavior: merge
   files:
   - ../base/nutanix-ccm.yaml
-
-bases:
-  - ../base/cluster-with-kcp.yaml
-  - ../base/secret.yaml
-  - ../base/cm.yaml
-  - ../base/nmt.yaml
-  - ../base/crs.yaml
-  - ../base/md.yaml
-  - ../base/mhc.yaml
-  - ../base/nutanix-ccm-crs.yaml
-  - ../base/nutanix-ccm-secret.yaml
-
-patchesStrategicMerge:
-  - ../base/ccm-patch.yaml
-  - ../base/cni-patch.yaml
+  name: nutanix-ccm
+resources:
+- ../base/cluster-with-kcp.yaml
+- ../base/secret.yaml
+- ../base/cm.yaml
+- ../base/nmt.yaml
+- ../base/crs.yaml
+- ../base/md.yaml
+- ../base/mhc.yaml
+- ../base/nutanix-ccm-crs.yaml
+- ../base/nutanix-ccm-secret.yaml
+patches:
+- path: ../base/ccm-patch.yaml
+- path: ../base/cni-patch.yaml

test/e2e/data/infrastructure-nutanix/v1alpha4/cluster-template/kustomization.yaml

@@ -1,5 +1,7 @@
-bases:
-  - ../bases/cluster-with-kcp.yaml
-  - ../bases/md.yaml
-  - ../bases/mhc.yaml
-  - ../bases/cm.yaml
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+resources:
+- ../bases/cluster-with-kcp.yaml
+- ../bases/md.yaml
+- ../bases/mhc.yaml
+- ../bases/cm.yaml

test/e2e/data/infrastructure-nutanix/v1alpha4/no-kubeproxy/cluster-template/kustomization.yaml

@@ -1,5 +1,6 @@
-bases:
-  - ../../cluster-template/
-
-patchesStrategicMerge:
-  - ../no-kubeproxy.yaml
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+resources:
+- ../../cluster-template/
+patches:
+- path: ../no-kubeproxy.yaml

test/e2e/data/infrastructure-nutanix/v1beta1/cluster-template-additional-categories/kustomization.yaml

@@ -1,5 +1,6 @@
-bases:
-  - ../cluster-template
-
-patchesStrategicMerge:
-  - ./nmt.yaml
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+resources:
+- ../cluster-template
+patches:
+- path: ./nmt.yaml

test/e2e/data/infrastructure-nutanix/v1beta1/cluster-template-clusterclass/kustomization.yaml

@@ -1,2 +1,4 @@
-bases:
-  - ../../../../../../templates/clusterclass/
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+resources:
+- ../../../../../../templates/clusterclass/