kustomize-controller v1.8.4: kustomize build produces stale output — new resources in resources: list not applied, removed resources persist

Environment

• flux: v2.8.0
• kustomize-controller: v1.8.4
• source-controller: v1.8.3

Description

When new entries are appended to a resources: list in kustomization.yaml, the kustomize-controller continues to produce the old build output: new resources are never applied, and resources previously removed from kustomization.yaml continue to appear as "unchanged" in server-side apply.

Structure

clusters/dev/apps.yaml → apps Kustomization: path ./apps/environments/dev/clusters/us

apps/environments/dev/clusters/us/kustomization.yaml resources:

• ../../base
• app1.yaml
• app2.yaml ← recently added, never applied

apps/environments/dev/base/kustomization.yaml resources:

• app3.yaml ← old entry, applied correctly
• app4.yaml ← recently added, never applied
• app5.yaml ← recently added, never applied

Steps to Reproduce

1. Have a Kustomization with path: ./apps/environments/dev/clusters/us where kustomization.yaml references ../../base
2. Add a new entry to ../../base/kustomization.yaml resources list
3. Commit and push
4. Run flux reconcile kustomization <name> --with-source

Expected Behavior

New resource appears in flux get kustomizations and is applied.

Actual Behavior

New resource is never created. The server-side apply completed log shows the same stale set of resources on every reconciliation.

Investigation

Verified that:

• The source-controller artifact tarball contains the correct, updated kustomization.yaml (extracted and checked with tar -xOf)
• Files for new resources (app5.yaml) exist in the tarball
• flux diff kustomization <name> shows no diff (treats stale build as current state)
• kubectl rollout restart deployment/kustomize-controller has no effect
• flux suspend source git flux-system && flux resume has no effect
• flux reconcile kustomization apps --with-source has no effect
• A previously deleted resource (app6, removed from kustomization.yaml weeks ago) still appears as "unchanged" in every server-side apply output — despite not being present in the tarball

Workaround

Manually creating the Kustomization CR with kubectl apply works correctly. The issue is specifically with the kustomize-controller's build phase not reflecting the current state of the artifact.