pytorch-operator: Consolidate manifests

[yanniszark]

Umbrella-Issue: kubeflow/manifests#1769

PyTorch Operator

Current manifests structure

.
├── crd.yaml
├── deployment.yaml
├── kustomization.yaml
├── namespace.yaml
├── podgroup.yaml
├── pytorch-job-crds
│   ├── base
│   └── overlays
│       └── application
├── pytorch-operator
│   ├── base
│   └── overlays
│       └── application

Explanation

• pytorch-job-crds and pytorch-job-operator came from kubeflow/manifests.
• The other files were the existing kustomization in the upstream repo.
• 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

The main diff is that the upstream manifests also install a namespace resource, which we don't want when installing with kubeflow. Following the standard base and overlays structure, I propose the following structure:

├── base
├── overlays
│   ├── kubeflow
│   └── standalone

• overlays/standalone is used to install the operator in its own namespace, for testing or other purposes.
• overlays/kubeflow is used to install the operator as part of kubeflow.

[yanniszark]

cc @kubeflow/wg-training-leads

[coveralls]

Coverage remained the same at 64.11% when pulling afb2445 on arrikto:feature-consolidate-manifests into 147349e on kubeflow:master.

[yanniszark]

/retest

[Jeffwan]

See #325 for more details. I file #326 to mitigate this issue. This should be unblocked once #326 is merged

[yanniszark]

I have rebased and the tests now pass. Thanks @Jeffwan

[Jeffwan]

/lgtm
/approve

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