Cannot delete DatadogAgent Resource

What happened:

In our KubernetesApp, I’m attempting to delete an obsolete DatadogAgent resource using the following kustomization.yaml file:

apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization
namespace: datadog

According to a plan preview, the resource appears as a deletion target, as shown below:

--- Last Deploy
+++ Head Commit

- 1. name="datadog", kind="DatadogAgent", namespace="datadog", apiVersion="datadoghq.com/v2alpha1"

However, when deploying with PipeCD, it’s determined that the deletion target resource does not exist, resulting in the manifest remaining undeleted:

[2024-08-09 12:39:15 +09:00]
Preparing deploy source at target commit (abd85be16f883b98b6b94e27e936d89b892ac279)
[2024-08-09 12:39:24 +09:00]
Successfully cloned the target commit
[2024-08-09 12:39:24 +09:00]
Successfully loaded the application configuration file
[2024-08-09 12:39:25 +09:00]
Successfully prepared deploy source at target commit (abd85be16f883b98b6b94e27e936d89b892ac279)
[2024-08-09 12:39:25 +09:00]
Loading manifests at commit abd85be16f883b98b6b94e27e936d89b892ac279 for handling
[2024-08-09 12:39:25 +09:00]
Successfully loaded 0 manifests
[2024-08-09 12:39:25 +09:00]
Start applying 0 manifests to "datadog" namespace
[2024-08-09 12:39:25 +09:00]
Successfully applied 0 manifests
[2024-08-09 12:39:25 +09:00]
Waiting for the applied manifests to be stable
[2024-08-09 12:39:40 +09:00]
Start finding all running resources but no longer defined in Git
[2024-08-09 12:39:40 +09:00]
Successfully loaded 0 live resources
[2024-08-09 12:39:40 +09:00]
There are no live resources should be removed

How can we delete the DatadogAgent resource as intended?

What you expected to happen:

We expect the DatadogAgent to be deleted.

How to reproduce it:

Environment:

• piped version: v0.48.3
• control-plane version:
• Others:

apiVersion: pipecd.dev/v1beta1
kind: KubernetesApp
spec:
  name: datadog-agent
  labels:
    env: REDACTED
    team: REDACTED
  input:
    namespace: datadog
    kustomizeVersion: 5.0.1
    kustomizeOptions:
      load-restrictor: "LoadRestrictionsNone"
  quickSync:
    prune: true

Start by reproducing the deployment with the KubernetesApp configuration, kustomization.yaml, and piped v0.48.3 described here. Trace the prune flow from loading zero manifests through finding live resources, then verify that an obsolete DatadogAgent is detected and deleted when prune is enabled.