Troubleshooting flux kustomization dependency

[eb112]

I'm having trouble with a relatively common pattern:

• Deploy infrastructure
• Deploy an application that has a dependency on a component of the infrastructure.

I know that if I make two Flux Kustomizations (apps and infrastructure), I should be able to use dependsOn to force Flux to deploy infrastructure first, then apps. However, I can't get it to work as I expect it to. I suspect I have a fundamental misunderstanding of FluxCD (and perhaps Kubernetes!).

Requirements:

• Application is a plain Kubernetes deployment.
• Application requires an HTTPRoute
• HTTPRoute requires CRDs and Gateway managed by infrastructure

Based on my understanding of how FluxCD handles plain YAML files, flux will automatically process the manifests in my application. Following concepts in the Kustomize Helm example I created two new Flux Kustomizations to gain control over the order in which infrastructure and apps and deployed.

However, when bootstrapping, FluxCD always processes the apps first, which causes the reconciliation to fail immediately.

Here's a truncated version of my infra and apps kustomizations. I've gone through multiple iterations using various intervals, timings, healthchecks, and wait flags. At this point, I'm not sure if I just haven't hit the magic combination, or if I'm essentially working with an anti-pattern of my own doing.

Note that if I remove ./apps from my repo, the infrastructure spins up fine. If I then add .apps/, the applications also work as expected. I just can't seem to do them all in a single bootstrap.

Here's a truncated version of my infra and apps kustomizations.

# ./infrastructure.yaml
apiVersion: kustomize.toolkit.fluxcd.io/v1
kind: Kustomization
metadata:
  name: infrastructure
  namespace: flux-system
spec:
  interval: 10m
  path: ./cluster/cluster/infrastructure
  prune: true
  wait: true
  timeout: 5m
  sourceRef:
    kind: GitRepository
    name: flux-system
  healthChecks:
    - apiVersion: helm.toolkit.fluxcd.io/v2beta1
      kind: HelmRelease
      name: traefik
      namespace: networking

# ./apps.yaml 
apiVersion: kustomize.toolkit.fluxcd.io/v1
kind: Kustomization
metadata:
  name: apps
  namespace: flux-system
spec:
  interval: 10m0s
  path: ./cluster/apps # applications in this directory and regular kubernetes deployment files.
  prune: true
  sourceRef:
    kind: GitRepository
    name: flux-system
  dependsOn:
    - name: infrastructure

Here's a truncated version of my repository structure:

cluster
├── apps
│   ├── my-application
│   │   ├── deployment.yaml # Plain YAML file
│   │   ├── kustomization.yaml
│   │   └── route.yaml #Plan YAML
│   └── kustomization.yaml
├── apps.yaml # kustomization of flux-system
├── flux-system
│   ├── gotk-components.yaml
│   ├── gotk-sync.yaml
│   └── kustomization.yaml
├── infrastructure
│   ├── kustomization.yaml
│   ├── networking
│   │   └── traefik
│   │       ├── kustomization.yaml
│   │       ├── release.yaml # HelmRelease
│   │       └── values.yaml
│   ├── sources
│   │   ├── gitrepositories.yaml
│   │   ├── helmrepositories.yaml
│   │   └── kustomization.yaml
└── infrastructure.yml #  kustomization of flux-system

Related error from flux logs:

2025-02-28T15:29:20.440Z error Kustomization/flux-system.flux-system - Reconciliation failed after 738.701414ms, next try in 10m0s HTTPRoute/my-application/my-application-route dry-run failed: no matches for kind "HTTPRoute" in version "gateway.networking.k8s.io/v1"

Possibly related issues / discussions:

• fluxcd not installing helm chart and crds #5177
• Help on Understanding a Dependency Misconfiguration #5172

Any hints pointing me in the right direction would be greatly appreciated.

(I do have a workaround where these resources are handled outside of flux, but I'm curious about what I'm missing).

eb