fix: correct the fluent-operator deployment to match the setup.yaml with helm template

[cw-Guo]

What this PR does / why we need it

Fixes the YAML-based installation regression reported in #1995.

Since #1953, manifests/setup/setup.yaml has been generated from the Kustomize configuration. However, the manager Deployment in config/manager/manager.yaml was not aligned with the Helm chart defaults.

The generated Deployment explicitly enabled the secure metrics endpoint on port 8443 while using a read-only root filesystem. Without a provided certificate, controller-runtime attempts to generate certificates under /tmp/k8s-metrics-server, which can prevent the operator from starting.

This PR aligns the default Kustomize Deployment with the Deployment produced by Helm:

• Uses the image's /manager entrypoint instead of overriding command.
• Removes the default leader-election and secure-metrics arguments.
• Uses the fluent-operator container name.
• Adds the default CONTAINER_LOG_PATH.
• Aligns resource limits, probes, container security context, and pod security context.
• Aligns the declared metrics port with Helm's default port 8080.
• Keeps HTTPS metrics configuration available as an optional Kustomize patch.

Which issue(s) this PR fixes

Fixes #1995

Files updated

• config/manager/manager.yaml

  • Aligns the Kustomize manager Deployment with the Helm defaults.

• config/default/kustomization.yaml

  • Stops enabling secure metrics by default.
  • Documents the optional patches required for HTTPS metrics with cert-manager.

• config/default/metrics_service.yaml

  • Changes the metrics Service from HTTPS port 8443 to the Helm default port 8080.

• manifests/setup/setup.yaml

  • Regenerates the published YAML installation bundle from the updated Kustomize configuration.

Validation

• Compared the generated Kustomize Deployment with the output of helm template using the default values.
• Ran make test-e2e: all 10 Fluentd e2e specs passed.
• Verified the operator Deployment becomes Ready in Kind with zero container restarts.
• Confirmed the operator uses the image entrypoint without explicit command or args.

Does this PR introduce a user-facing change?

Fix the YAML-based installation by aligning the generated operator Deployment with the Helm chart defaults.

[Copilot]

Pull request overview

This PR updates the Kustomize-based installation manifests to align the Fluent Operator manager Deployment and metrics Service with the Helm chart defaults, addressing a startup regression caused by secure metrics certificate generation on a read-only filesystem.

Changes:

• Aligns the manager Deployment spec (entrypoint usage, container name, env, probes, resources, and security contexts) with Helm defaults.
• Switches the metrics Service from HTTPS/8443 to a metrics port on 8080 and documents HTTPS metrics as an optional patch path.
• Regenerates the published manifests/setup/setup.yaml bundle from the updated Kustomize config.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 3 comments.

File	Description
config/manager/manager.yaml	Reworks the manager Deployment to match Helm defaults (entrypoint/args, ports, security context, probes, resources).
config/default/kustomization.yaml	Stops enabling secure metrics by default and updates guidance for optional HTTPS metrics patches.
config/default/metrics_service.yaml	Changes the metrics Service port/name to metrics:8080.
manifests/setup/setup.yaml	Regenerated install bundle reflecting the updated Kustomize Deployment and Service.

[marcofranssen]

CI fails.

https://github.com/fluent/fluent-operator/actions/runs/30819768575/job/91706436277?pr=2025

CI fails