diff --git a/clustertool/embed/generic/kubernetes/core/kyverno-policies/ks.yaml b/clustertool/embed/generic/kubernetes/core/kyverno-policies/ks.yaml
deleted file mode 100644
index e0dd28c8960..00000000000
--- a/clustertool/embed/generic/kubernetes/core/kyverno-policies/ks.yaml
+++ /dev/null
@@ -1,12 +0,0 @@
-apiVersion: kustomize.toolkit.fluxcd.io/v1
-kind: Kustomization
-metadata:
-  name: kyverno-policies
-  namespace: flux-system
-spec:
-  interval: 10m
-  path: clusters/main/kubernetes/core/kyverno-policies/app
-  prune: true
-  sourceRef:
-    kind: GitRepository
-    name: cluster
diff --git a/clustertool/embed/generic/kubernetes/core/system-upgrade-controller-plans/ks.yaml b/clustertool/embed/generic/kubernetes/core/system-upgrade-controller-plans/ks.yaml
deleted file mode 100644
index 16b422cab93..00000000000
--- a/clustertool/embed/generic/kubernetes/core/system-upgrade-controller-plans/ks.yaml
+++ /dev/null
@@ -1,19 +0,0 @@
----
-apiVersion: kustomize.toolkit.fluxcd.io/v1
-kind: Kustomization
-metadata:
-  name: system-upgrade-controller-plans
-  namespace: flux-system
-spec:
-  interval: 10m
-  path: clusters/main/kubernetes/core/system-upgrade-controller-plans/app
-  prune: true
-  sourceRef:
-    kind: GitRepository
-    name: cluster
-  targetNamespace: system-upgrade
-  dependsOn:
-  - name: system-upgrade-controller
-  wait: false
-  retryInterval: 1m
-  timeout: 5m
diff --git a/clustertool/embed/generic/kubernetes/system/kyverno/ks.yaml b/clustertool/embed/generic/kubernetes/system/kyverno/ks.yaml
deleted file mode 100644
index c96e462bfa9..00000000000
--- a/clustertool/embed/generic/kubernetes/system/kyverno/ks.yaml
+++ /dev/null
@@ -1,12 +0,0 @@
-apiVersion: kustomize.toolkit.fluxcd.io/v1
-kind: Kustomization
-metadata:
-  name: kyverno
-  namespace: flux-system
-spec:
-  interval: 10m
-  path: clusters/main/kubernetes/system/kyverno/app
-  prune: true
-  sourceRef:
-    kind: GitRepository
-    name: cluster
diff --git a/clustertool/embed/generic/kubernetes/system/system-upgrade-controller/ks.yaml b/clustertool/embed/generic/kubernetes/system/system-upgrade-controller/ks.yaml
deleted file mode 100644
index a5c4af1fd38..00000000000
--- a/clustertool/embed/generic/kubernetes/system/system-upgrade-controller/ks.yaml
+++ /dev/null
@@ -1,13 +0,0 @@
----
-apiVersion: kustomize.toolkit.fluxcd.io/v1
-kind: Kustomization
-metadata:
-  name: system-upgrade-controller
-  namespace: flux-system
-spec:
-  interval: 10m
-  path: clusters/main/kubernetes/system/system-upgrade-controller/app
-  prune: true
-  sourceRef:
-      kind: GitRepository
-      name: cluster