chore: standardize controller kustomize implementation

[andyatmiami]

ℹ️ NO GH ISSUE

Motivation:

This refactoring aligns the controller's kustomize configuration with best practices and ensures consistency with other components (backend, frontend). The primary goals were:

• Remove nested subdirectories (bases/, patches/) to match the flat structure used in other base directories
• Ensure components are only included in overlays, not the base
• Improve maintainability through consistent naming conventions
• Better organize resources by their purpose and dependencies

Changes Made:

1. Flattened CRD directory structure:

   • Moved CRD base files from crd/bases/ to crd/
   • Moved patch files from crd/patches/ to crd/
   • Updated all references in Makefile and test files

2. Standardized patch file naming:

   • Renamed cainjection_in_*.yaml → *_cainjection_patch.yaml
   • Renamed webhook_in_*.yaml → *_webhook_patch.yaml
   • Provides consistent naming pattern across all patches

3. Component organization:

   • Moved metrics_service.yaml to prometheus component (only included when prometheus is enabled)
   • Moved manager_webhook_patch.yaml to certmanager component (only needed when cert-manager is enabled)
   • Extracted namespace.yaml from manager.yaml for explicit definition

4. Updated references:

   • Makefile: Changed controller-gen output path from crd/bases to crd
   • Test files: Updated CRDDirectoryPaths in controller, webhook, and backend test suites

5. Removed unused build-installer target:

   • Removed from Makefile and README as it's not used and kustomize provides better facilities for vendoring

Expected Manifest Output Differences:

1. webhook-service port now has name attribute:

   • Added name: webhook to the port definition
   • This enables replacements to reference the port by name, improving maintainability and keeping port values in sync between Service and Deployment

2. workspaces-controller-metrics-service is missing:

   • This is expected as metrics_service.yaml was moved to the prometheus component
   • The service will only appear when the prometheus component is explicitly enabled in an overlay

3. kubeflow-workspaces-istio-config ConfigMap labels:

   • Common labels were added (app.kubernetes.io/managed-by, app.kubernetes.io/name, app.kubernetes.io/part-of) due to reordering of components in the overlay
   • The common component is now applied last to ensure its labels are applied to all resources consistently

4. All other resources remain functionally equivalent:

   • CRDs, Deployments, Services, RBAC, and webhook configurations are unchanged in functionality
   • Only structural and organizational improvements were made

[google-oss-prow]

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[andyatmiami]

/ok-to-test