fix: don't strip user-managed kagenti.io/skills annotation on deletion

The deletion handler was removing the kagenti.io/skills annotation from
the target Deployment. This annotation is user-managed (set by the
kagenti backend or user) — the operator reads but never sets it, so it
should not remove it either.

This caused the E2E skill discovery test to fail: the "feature gate
disabled" test deletes the AgentRuntime, the finalizer strips the
annotation, and the subsequent "feature gate enabled" test finds an
empty annotation on the same Deployment.

Also re-apply the Deployment fixture in the E2E "feature gate enabled"
BeforeAll to guard against any future annotation-stripping regressions.

Assisted-By: Claude (Anthropic AI) <noreply@anthropic.com>
Signed-off-by: Paolo Dettori <dettori@us.ibm.com>

Author: pdettori

kagenti-operator/internal/controller/agentruntime_controller.go

@@ -719,10 +719,6 @@ func (r *AgentRuntimeReconciler) handleDeletion(ctx context.Context, rt *agentv1
 			delete(workloadLabels, LabelManagedBy)
 			acc.obj.SetLabels(workloadLabels)
 
-			// Remove skills annotation from workload metadata.
-			workloadAnnotations := acc.obj.GetAnnotations()
-			delete(workloadAnnotations, AnnotationSkills)
-			acc.obj.SetAnnotations(workloadAnnotations)
 
 			// Remove kagenti.io/type from PodTemplateSpec pod labels so future pods
 			// are not presented to the webhook with the type label.

kagenti-operator/test/e2e/e2e_test.go

@@ -2133,6 +2133,13 @@ rules:
 
 	Context("Feature gate enabled", Ordered, func() {
 		BeforeAll(func() {
+			By("re-applying target Deployment to restore skills annotation after prior deletion cleanup")
+			_, err := utils.KubectlApplyStdin(skillDiscoveryDeploymentFixture(), skillDiscoveryTestNamespace)
+			Expect(err).NotTo(HaveOccurred())
+			Expect(utils.WaitForDeploymentReady(
+				"skill-discovery-agent", skillDiscoveryTestNamespace, 2*time.Minute,
+			)).To(Succeed())
+
 			By("enabling skillDiscovery feature gate")
 			Expect(utils.EnableSkillDiscovery(controllerNamespace, controllerDeployment)).To(Succeed())