fix: Argo CD bootstrap normalization -- adopt cert-manager/Authentik config, fix policy drift

Stage 5 + part of Stage 6/7 of REFACTOR_PLAN.md. This is the highest-risk
stage per the plan -- these Applications are NOT to be pushed/synced blindly.
Each needs `kubectl diff` against live state one at a time before enabling.

New Applications (previously-live resources with zero GitOps coverage):
- cert-manager-config.yaml (manifests/cert-manager: both ClusterIssuers + the
  internal CA Certificate -- every TLS cert in the cluster depends on these,
  and nothing currently restores them on a cold rebuild).
- authentik-config.yaml (manifests/authentik: ingress, proxy outpost,
  middleware -- raw manifests only, low risk).
- authentik.yaml (the Authentik Helm chart itself): sync is deliberately left
  MANUAL and targetRevision is a REPLACE_ME placeholder -- I don't have a safe
  way to read the live chart version (`helm list -n authentik`), and guessing
  wrong risks an unwanted upgrade/downgrade of the SSO IdP gating Argo CD/
  Grafana/Gitea logins. Needs your input before this one goes anywhere.
- network.yaml: widens coverage to the 4 non-sealed files in manifests/network
  (ddns-cronjob, glances-debian-ingress, traefik-dashboard-ingress,
  watch-party-ingress) that were previously invisible to Argo CD; keeps
  network-secrets.yaml scoped to *-sealed.yaml only.

Fixes:
- homeassistant.yaml: destination.namespace was "homeassistant" (empty,
  unused) while the actual resources are hardcoded to "default" -- corrected,
  dropped CreateNamespace=true. The old empty namespace isn't auto-deleted
  (prune: false); safe to remove by hand if desired.
- gitea-backup.yaml: added the missing Namespace object (nothing created
  "gitea-backup" before); replaced a cluster-wide ClusterRole/ClusterRoleBinding
  granting pods/exec everywhere with a Role/RoleBinding scoped to the `gitea`
  namespace, matching what the backup script actually execs into. NOTE: this
  is already under active sync via gitea-secrets.yaml (selfHeal: true,
  prune: false) -- once pushed, the old ClusterRole/ClusterRoleBinding will
  need manual `kubectl delete` since Argo CD won't prune them.
- Added sync-wave "-2" to cert-manager/sealed-secrets Applications so their
  CRDs land before consumers (matches the existing -1/0 wave pattern).
- Normalized targetRevision HEAD -> main on home-services/otel-collector/tempo.
- Normalized sync policy per your decision: home-services/otel-collector/tempo
  prune true -> false; pihole/pihole-debian selfHeal false -> true (repo-wide
  consistency, per your call on finding #18).

Verified: kubeconform valid across all manifests + Argo CD Application objects.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

argocd/apps/authentik-config.yaml

@@ -0,0 +1,20 @@
+apiVersion: argoproj.io/v1alpha1
+kind: Application
+metadata:
+  name: authentik-config
+  namespace: argocd
+spec:
+  project: default
+  source:
+    repoURL: https://gitea.nik4nao.com/nik/homelab.git
+    targetRevision: main
+    path: manifests/authentik
+    directory:
+      include: '*.yaml'
+  destination:
+    server: https://kubernetes.default.svc
+    namespace: authentik
+  syncPolicy:
+    automated:
+      prune: false
+      selfHeal: true

argocd/apps/authentik.yaml

@@ -0,0 +1,33 @@
+# NEEDS YOUR INPUT before first sync: targetRevision below is a placeholder.
+# Run `helm list -n authentik` on the live cluster and set this to the chart
+# version actually deployed (installed by hand per the header comment in
+# values/authentik.yaml) -- Authentik is the SSO IdP gating Argo CD/Grafana/
+# Gitea logins, so adopting it into GitOps with the wrong version could
+# trigger an unwanted live chart upgrade/downgrade on first sync. Sync is
+# left manual (no `automated:` block) until you've confirmed this and diffed
+# with `kubectl diff` / `argocd app diff`.
+apiVersion: argoproj.io/v1alpha1
+kind: Application
+metadata:
+  name: authentik
+  namespace: argocd
+  annotations:
+    argocd.argoproj.io/sync-wave: "-1"
+spec:
+  project: default
+  sources:
+    - repoURL: https://charts.goauthentik.io
+      chart: authentik
+      targetRevision: "REPLACE_ME"
+      helm:
+        valueFiles:
+          - $values/values/authentik.yaml
+    - repoURL: https://gitea.nik4nao.com/nik/homelab.git
+      targetRevision: main
+      ref: values
+  destination:
+    server: https://kubernetes.default.svc
+    namespace: authentik
+  syncPolicy:
+    syncOptions:
+      - CreateNamespace=true

argocd/apps/cert-manager-config.yaml

@@ -0,0 +1,22 @@
+apiVersion: argoproj.io/v1alpha1
+kind: Application
+metadata:
+  name: cert-manager-config
+  namespace: argocd
+  annotations:
+    argocd.argoproj.io/sync-wave: "-1"
+spec:
+  project: default
+  source:
+    repoURL: https://gitea.nik4nao.com/nik/homelab.git
+    targetRevision: main
+    path: manifests/cert-manager
+    directory:
+      include: '*.yaml'
+  destination:
+    server: https://kubernetes.default.svc
+    namespace: cert-manager
+  syncPolicy:
+    automated:
+      prune: false
+      selfHeal: true

argocd/apps/cert-manager.yaml

@@ -3,6 +3,8 @@ kind: Application
 metadata:
   name: cert-manager
   namespace: argocd
+  annotations:
+    argocd.argoproj.io/sync-wave: "-2"
 spec:
   project: default
   sources:

argocd/apps/home-services.yaml

@@ -9,14 +9,14 @@ spec:
   project: default
   source:
     repoURL: https://gitea.nik4nao.com/nik/homelab.git
-    targetRevision: HEAD
+    targetRevision: main
     path: manifests/home-services
   destination:
     server: https://kubernetes.default.svc
     namespace: home-services
   syncPolicy:
     automated:
-      prune: true
+      prune: false
       selfHeal: true
     syncOptions:
       - CreateNamespace=true

argocd/apps/homeassistant.yaml

@@ -11,10 +11,8 @@ spec:
     path: manifests/homeassistant
   destination:
     server: https://kubernetes.default.svc
-    namespace: homeassistant
+    namespace: default
   syncPolicy:
     automated:
       prune: false
       selfHeal: true
-    syncOptions:
-      - CreateNamespace=true

argocd/apps/network.yaml

@@ -0,0 +1,23 @@
+apiVersion: argoproj.io/v1alpha1
+kind: Application
+metadata:
+  name: network
+  namespace: argocd
+spec:
+  project: default
+  source:
+    repoURL: https://gitea.nik4nao.com/nik/homelab.git
+    targetRevision: main
+    path: manifests/network
+    directory:
+      exclude: '*-sealed.yaml'
+      include: '*.yaml'
+  destination:
+    server: https://kubernetes.default.svc
+    namespace: pihole
+  syncPolicy:
+    automated:
+      prune: false
+      selfHeal: true
+    syncOptions:
+      - CreateNamespace=true

argocd/apps/otel-collector.yaml

@@ -14,14 +14,14 @@ spec:
         valueFiles:
           - $values/values/otel-collector.yaml
     - repoURL: https://gitea.nik4nao.com/nik/homelab.git
-      targetRevision: HEAD
+      targetRevision: main
       ref: values
   destination:
     server: https://kubernetes.default.svc
     namespace: monitoring
   syncPolicy:
     automated:
-      prune: true
+      prune: false
       selfHeal: true
     syncOptions:
       - CreateNamespace=false

argocd/apps/pihole-debian.yaml

@@ -21,6 +21,6 @@ spec:
   syncPolicy:
     automated:
       prune: false
-      selfHeal: false
+      selfHeal: true
     syncOptions:
       - CreateNamespace=true

argocd/apps/pihole.yaml

@@ -21,6 +21,6 @@ spec:
   syncPolicy:
     automated:
       prune: false
-      selfHeal: false
+      selfHeal: true
     syncOptions:
       - CreateNamespace=true

argocd/apps/sealed-secrets.yaml

@@ -3,6 +3,8 @@ kind: Application
 metadata:
   name: sealed-secrets
   namespace: argocd
+  annotations:
+    argocd.argoproj.io/sync-wave: "-2"
 spec:
   project: default
   sources:

argocd/apps/tempo.yaml

@@ -14,14 +14,14 @@ spec:
         valueFiles:
           - $values/values/tempo.yaml
     - repoURL: https://gitea.nik4nao.com/nik/homelab.git
-      targetRevision: HEAD
+      targetRevision: main
       ref: values
   destination:
     server: https://kubernetes.default.svc
     namespace: monitoring
   syncPolicy:
     automated:
-      prune: true
+      prune: false
       selfHeal: true
     syncOptions:
       - CreateNamespace=false

manifests/gitea/gitea-backup.yaml

@@ -2,15 +2,21 @@
 # Delete: kubectl delete -f manifests/gitea/gitea-backup.yaml
 # Description: CronJob that backs up Gitea to NFS every 7 days, with RBAC and PV/PVC.
 apiVersion: v1
+kind: Namespace
+metadata:
+  name: gitea-backup
+---
+apiVersion: v1
 kind: ServiceAccount
 metadata:
   name: gitea-backup
   namespace: gitea-backup
 ---
 apiVersion: rbac.authorization.k8s.io/v1
-kind: ClusterRole
+kind: Role
 metadata:
   name: gitea-backup
+  namespace: gitea
 rules:
   - apiGroups: [""]
     resources: ["pods"]
@@ -20,15 +26,16 @@ rules:
     verbs: ["create"]
 ---
 apiVersion: rbac.authorization.k8s.io/v1
-kind: ClusterRoleBinding
+kind: RoleBinding
 metadata:
   name: gitea-backup
+  namespace: gitea
 subjects:
   - kind: ServiceAccount
     name: gitea-backup
     namespace: gitea-backup
 roleRef:
-  kind: ClusterRole
+  kind: Role
   name: gitea-backup
   apiGroup: rbac.authorization.k8s.io
 ---