MLE-25053 update config readme and sample files

[pengzhouml]

No description provided.

[Copilot]

Pull Request Overview

This PR updates configuration files to upgrade the fluent-bit container image from version 3.2.5 to 4.1.1, modifies sample configurations, and makes minor adjustments to build and documentation files.

Key changes include:

• Upgrading fluent-bit image version across test files, CRDs, sample configs, and API type definitions
• Updating log collection output configuration format from INI-style to YAML-style syntax
• Enabling persistence by default in quick-start sample and removing hugepages configuration from complete sample

Reviewed Changes

Copilot reviewed 16 out of 18 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
test/e2e/2_marklogic_cluster_test.go	Updates fluent-bit version in e2e test configuration
internal/controller/marklogicgroup_controller_test.go	Updates fluent-bit version constant and test instantiation
internal/controller/marklogiccluster_controller_test.go	Updates fluent-bit version in cluster controller test
config/samples/quick-start.yaml	Enables persistence by default
config/samples/minimal-production.yaml	Updates fluent-bit version and converts output config to YAML format
config/samples/complete.yaml	Updates fluent-bit version, converts output config to YAML, and removes hugepages entries
config/crd/kustomization.yaml	Comments out patches configuration line
config/crd/bases/marklogic.progress.com_marklogicgroups.yaml	Updates default fluent-bit version in CRD
config/crd/bases/marklogic.progress.com_marklogicclusters.yaml	Updates default fluent-bit version in CRD
charts/marklogic-operator-kubernetes/templates/marklogicgroup-crd.yaml	Updates default fluent-bit version in Helm chart template
charts/marklogic-operator-kubernetes/templates/marklogiccluster-crd.yaml	Updates default fluent-bit version in Helm chart template
api/v1/marklogicgroup_types.go	Updates default fluent-bit version in type definition
api/v1/marklogiccluster_types.go	Updates default fluent-bit version in type definition
api/v1/common_types.go	Updates default fluent-bit version in common types
README.md	Updates version numbers and security vulnerability notes
Makefile	Removes commented line and adds platform flag to docker build

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[rwinieski]

We should keep the huge pages in the complete yaml file.

[pengzhouml]

I've made the fix. Will Try to merge to release branch for now