XGBoost Operator: Refactor manifests structure

[yanniszark]

Umbrella-Issue: kubeflow/manifests#1769

XGBoost Operator

Current manifests structure

manifests
└── xgboost-operator
    ├── base
    └── overlays
        └── application

Explanation

• The application overlays contain Application CRs, which we want to move away from (Why do we need kubernetes-sigs/application controller in Kubeflow? manifests#1715 (comment))

Recommended end state

manifests
├── base
└── overlays
    └── kubeflow

In the future, we'd like base to import the kubebuilder-generated manifests.

[yanniszark]

cc @kubeflow/wg-training-leads

[terrytangyuan]

Could we stick with kubectl kustomize?

[yanniszark]

@terrytangyuan sure! I removed it because it uses a deprecated kustomize version.

[terrytangyuan]

/lgtm
/approve

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