refactor(apps): split monolithic apps Kustomization into dependency waves

Replaces the single `apps` Flux Kustomization with dependency-ordered waves
(apps-wave-0..2) so a crashlooping workload isolates to its wave + downstream
instead of stalling the entire app tier. Parallel within a wave, ordered across.

- catalog/render.py: compute waves by longest dependency-path depth over the
  ServiceDefinition `dependencies:` edges (a `<svc>-db` is a leaf, so its
  consumer lands strictly higher — the "DB below consumer" rule falls out of
  longest-path, no special case). `--emit-waves` generates the per-wave
  kustomizations + Flux CRs; `--wave-layout` places renders into the right dir.
  wave 0: pihole gitea jackett plex qbittorrent nextcloud-db semaphore-db
  wave 1: sonarr radarr nextcloud semaphore gitea-actions
  wave 2: seerr
- apps/*.yaml -> apps/wave-{0,1,2}/ (byte-identical moves; SOPS files intact).
- clusters/base: apps.yaml removed; apps-wave-{0,1,2}.yaml added (dependsOn
  chain: platform-config -> wave-0 -> wave-1 -> wave-2, prune+wait each).
- clusters/dev: one SOPS decryption patch per wave (load-bearing).
- DESIGN-waves.md: wave table, topology, cutover runbook.

Cutover: preceded by disabling prune on `apps` (1bfb0db) so removing that
object here does not GC its resources; the wave Kustomizations SSA-adopt the
byte-identical manifests in place (no restart, no PVC churn).

Co-Authored-By: Claude Opus 4.8 <[email protected]>

clusters/dev/kustomization.yaml

@@ -26,11 +26,37 @@ patches:
           provider: sops
           secretRef:
             name: sops-age
+  # SOPS decryption on EACH app wave (the app tier is now apps-wave-0..N, not a single `apps`
+  # Kustomization). Same stanza the retired `apps` Kustomization received — one per wave, by
+  # name. Add a patch here whenever `render.py --emit-waves` introduces a new deepest wave
+  # (DESIGN-waves.md cutover note). The `sops-age` Secret is created out-of-band (name only).
   - patch: |-
       apiVersion: kustomize.toolkit.fluxcd.io/v1
       kind: Kustomization
       metadata:
-        name: apps
+        name: apps-wave-0
+        namespace: flux-system
+      spec:
+        decryption:
+          provider: sops
+          secretRef:
+            name: sops-age
+  - patch: |-
+      apiVersion: kustomize.toolkit.fluxcd.io/v1
+      kind: Kustomization
+      metadata:
+        name: apps-wave-1
+        namespace: flux-system
+      spec:
+        decryption:
+          provider: sops
+          secretRef:
+            name: sops-age
+  - patch: |-
+      apiVersion: kustomize.toolkit.fluxcd.io/v1
+      kind: Kustomization
+      metadata:
+        name: apps-wave-2
         namespace: flux-system
       spec:
         decryption: