fix: resolve cert-manager CRD dependency for cluster redeployability

- Add root kustomization.yaml to explicitly list included paths
- Exclude cert-manager and cert-manager-issuer from root kustomization
- Add Flux Kustomizations in system/flux/ to manage deployment order
- cert-manager Flux Kustomization includes health checks for CRDs
- cert-manager-issuer depends on cert-manager being ready

kubernetes/system/cert-manager-issuer/clusterissuer.yaml

@@ -0,0 +1,24 @@
+# Let's Encrypt ClusterIssuer
+# Supports multiple DNS providers via DNS-01 challenge
+
+apiVersion: cert-manager.io/v1
+kind: ClusterIssuer
+metadata:
+  name: letsencrypt-production
+spec:
+  acme:
+    server: https://acme-v02.api.letsencrypt.org/directory
+    email: vhaudiquet343@hotmail.fr
+    privateKeySecretRef:
+      name: letsencrypt-production-account-key
+    solvers:
+      # Cloudflare solver for vhaudiquet.fr and buildpath.win
+      - dns01:
+          cloudflare:
+            apiTokenSecretRef:
+              name: cloudflare-api-token
+              key: api-token
+        selector:
+          dnsZones:
+            - vhaudiquet.fr
+            - buildpath.win