Fix deprecations in kustomizations

[friegger]

Fixes #589

Summary by CodeRabbit

• Chores
  • Standardized Kubernetes Kustomize manifests with explicit API versions and resource types.
  • Updated deployment configuration to target the kube-system namespace.
  • Modernized patch configuration and secret file declarations for improved compatibility with current Kustomize tooling.
  • Simplified the default deployment resource selection.
  • Reformatted RBAC resource definitions without changing their behavior.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: d164a4c2-a621-4eba-bc1e-f765d45b6903

📥 Commits

Reviewing files that changed from the base of the PR and between 30a8ee1 and 40f2c65.

📒 Files selected for processing (5)

• config/config/kustomization.yaml
• config/default/kustomization.yaml
• config/kind/kustomization.yaml
• config/manager/kustomization.yaml
• config/rbac/kustomization.yaml

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📝 Walkthrough

Walkthrough

Changes

Kustomization updates

Layer / File(s)	Summary
Manifest metadata and resource declarations config/config/kustomization.yaml, config/default/kustomization.yaml, config/manager/kustomization.yaml, config/rbac/kustomization.yaml	Kustomization metadata is made explicit, resource references are preserved or narrowed, and RBAC resource formatting is updated.
Kind Kustomize field migration config/kind/kustomization.yaml	The manifest adopts v1beta1, replaces patchesStrategicMerge with patches, and preserves the generated secret sources and names.

Estimated code review effort: 2 (Simple) | ~10 minutes

Possibly related issues

• ironcore-dev/libvirt-provider#757 — Covers the same Kustomize deprecation migration from patchesStrategicMerge to patches.
• ironcore-dev/ceph-provider#905 — Covers equivalent Kustomize manifest updates and deprecated patch-field replacement.
• ironcore-dev/ironcore#1521 — Directly matches the config/kind/kustomization.yaml deprecation fix.

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Description check	⚠️ Warning	The description only says "Fixes #589" and is missing the required Proposed Changes section.	Add the three Proposed Changes bullets and keep the Fixes # line so the template is complete.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly matches the main change: fixing deprecated kustomization usage.
Linked Issues check	✅ Passed	The PR replaces patchesStrategicMerge with patches, matching the linked issue's deprecation fix.
Out of Scope Changes check	✅ Passed	The edits stay within kustomization manifests and deprecation cleanup, with no clearly unrelated changes.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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