ignoreDifferences is not automatically refreshed.

[mulhotavares]

Checklist:

• I've searched in the docs and FAQ for my answer: https://bit.ly/argocd-faq.
• I've included steps to reproduce the bug.
• I've pasted the output of argocd version.

Describe the bug
When applying a helm chart that only contains CRDs, it will show OutOfSync due to a diff in the manifests.
When I add the ignoreDifferences to ignore that mismatch, and hit Sync, the application still shows as OutOfSync, until I click refresh.

To Reproduce
Create a new App via UI. Click Edit as YAML. Paste this code:

apiVersion: argoproj.io/v1alpha1
kind: Application
metadata:
  name: my-test-app
spec:
  destination:
    namespace: test-crds
    server: 'https://kubernetes.default.svc'
  source:
    repoURL: 'https://helm.linkerd.io/stable'
    targetRevision: 1.4.0
    chart: linkerd-crds
  project: cluster-infra
  syncPolicy:
    automated: null
    syncOptions:
      - CreateNamespace=true

Then Save, Create, and Sync.
After sync, everything will be OutOfSync. Click on refresh, and a few of them become in Sync. (Also a bug here)

If you inspect the diff, you should see only this:

Now go to App Details -> Manifest and click EDIT. Right in the end, paste this:

ignoreDifferences:
  - group: apiextensions.k8s.io
    kind: CustomResourceDefinition
    jsonPointers:
      - /spec/names/shortNames

Hit Save, close it and sync.
The application will still be OutOfSync.
Clicking refresh will make mark it as synced.

Expected behavior

After setting ignoreDifferences I'd expect the refresh to be automatic.

Screenshots

Version
Please note the version below seems incorrect. See screenshot:

argocd version
argocd: v2.6.2+6e02f8b.dirty
  BuildDate: 2023-02-16T18:43:27Z
  GitCommit: 6e02f8b23201b0620a4ff1bce5d38229ba1eb02e
  GitTreeState: dirty
  GoVersion: go1.19.6
  Compiler: gc
  Platform: darwin/arm64
argocd-server: v2.6.2+6e02f8b.dirty
  BuildDate: 2023-02-16T18:43:27Z
  GitCommit: 6e02f8b23201b0620a4ff1bce5d38229ba1eb02e
  GitTreeState: dirty
  GoVersion: go1.19.6
  Compiler: gc
  Platform: darwin/arm64
  Kustomize Version: v4.5.7 2022-08-02T16:28:01Z
  Helm Version: v3.10.0+gce66412
  Kubectl Version: v0.24.2
  Jsonnet Version: v0.19.1

Logs

Paste any relevant application logs here.

[rufreakde]

Encountering the same issue with argocd version 2.3.17. It seems the CRDs get changed when applied because of the empty list and hence are never in sync.