Move kustomize manifests a dedicate directory

[IronPan]

We will have a side by side directory for HELM registry in the future for GCP marketplace deployment.

Also bump the API version for K8s resources for consistency.

/assign @neuromage

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This change is 

[Ark-kun]

/lgtm

[IronPan]

/approve

[IronPan]

/test kubeflow-pipeline-e2e-test

[k8s-ci-robot]

@IronPan: The following test failed, say /retest to rerun them all:

Test name	Commit	Details	Rerun command
kubeflow-pipeline-e2e-test	819dc4f	link	/test kubeflow-pipeline-e2e-test

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[neuromage]

/lgtm
/approve

[k8s-ci-robot]

[APPROVALNOTIFIER] This PR is APPROVED

This pull-request has been approved by: IronPan, neuromage

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