feat(atlantis): migrate remaining 13 namespaces to flux/ pattern, retire cluster-apps

Move actions-runner-system, cert-manager, cnpg-system, db, default,
envoy-gateway-system, external-dns, garage, gateway, gateway-system,
it-tools, kube-system, and rook-ceph each to a flux/<ns>.yaml file
with Namespace + {ns}-apps parent FK (wait: false). External-secrets-
dependent namespaces dependsOn external-secrets-apps. rook-ceph keeps
the privileged PSS labels.

Drop components/common and Namespace patches from each apps/<ns>/
kustomization.yaml. Remove the now-unused apps/default/namespace.yaml,
apps/kustomization.yaml, and flux/apps.yaml (cluster-apps wiring).

Live FKs in all 13 namespaces were suspended out-of-band so cluster-apps'
removal doesn't cascade-delete their managed resources during takeover.

Author: nicolerenee

kubernetes/clusters/atlantis-k8s01/apps/actions-runner-system/kustomization.yaml

@@ -4,7 +4,6 @@ apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 namespace: actions-runner-system
 components:
-  - ../../../../components/common
   - ../../../../components/flux-post-build-variables
 resources:
   - ./actions-runner-controller.yaml

kubernetes/clusters/atlantis-k8s01/apps/cert-manager/kustomization.yaml

@@ -4,7 +4,6 @@ apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 namespace: cert-manager
 components:
-  - ../../../../components/common
   - ../../../../components/flux-post-build-variables
 resources:
   - ./cert-manager.yaml

kubernetes/clusters/atlantis-k8s01/apps/cnpg-system/kustomization.yaml

@@ -4,7 +4,6 @@ apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 namespace: cnpg-system
 components:
-  - ../../../../components/common
   - ../../../../components/flux-post-build-variables
 resources:
   - ./cloudnative-pg.yaml

kubernetes/clusters/atlantis-k8s01/apps/db/kustomization.yaml

@@ -4,7 +4,6 @@ apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 namespace: db
 components:
-  - ../../../../components/common
   - ../../../../components/flux-post-build-variables
 resources:
   - ./cloudnative-pg.yaml

kubernetes/clusters/atlantis-k8s01/apps/default/kustomization.yaml

@@ -3,8 +3,9 @@
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 namespace: default
+components:
+  - ../../../../components/flux-post-build-variables
 resources:
   - ./app-template.yaml
   - ./k8s-cluster-info.yaml
   - ./k8s-cluster-secrets.yaml
-  - ./namespace.yaml

kubernetes/clusters/atlantis-k8s01/apps/default/namespace.yaml

@@ -4,7 +4,6 @@ apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 namespace: envoy-gateway-system
 components:
-  - ../../../../components/common
   - ../../../../components/flux-post-build-variables
 resources:
   - ./envoy-gateway.yaml

kubernetes/clusters/atlantis-k8s01/apps/envoy-gateway-system/kustomization.yaml

@@ -4,7 +4,6 @@ apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 namespace: external-dns
 components:
-  - ../../../../components/common
   - ../../../../components/flux-post-build-variables
 resources:
   - ./cloudflare.yaml

kubernetes/clusters/atlantis-k8s01/apps/external-dns/kustomization.yaml

@@ -4,7 +4,6 @@ apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 namespace: garage
 components:
-  - ../../../../components/common
   - ../../../../components/flux-post-build-variables
 resources:
   - ./nas-garage.yaml

kubernetes/clusters/atlantis-k8s01/apps/garage/kustomization.yaml

@@ -4,7 +4,6 @@ apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 namespace: gateway-system
 components:
-  - ../../../../components/common
   - ../../../../components/flux-post-build-variables
 resources:
   - ./gateways.yaml