Refactor structure for Flux v2.7

[stefanprodan]

Changelog

Migration to FluxInstance CRD

• Added kubernetes/clusters/local/instance.yaml with FluxInstance configuration
• Replaced Helm-based Flux Operator and Flux installation with flux-operator install command
• Removed Helm as a dependency (no longer required)

CLI Tooling

• Integrated Flux Operator CLI throughout the project
• Added make ls command to list deployed resources using flux-operator tree
• Updated GitHub Actions workflow to install Flux Operator CLI

Simplified Bootstrap Process (scripts/flux-up.sh)

• Replaced 66 lines of Helm installation logic with direct FluxInstance installation
• Changed from kubectl wait to flux-operator wait for better readability
• Streamlined cluster bootstrap process

Infrastructure Cleanup

• Deleted kubernetes/infra/flux-operator.yaml (replaced by flux-operator install that setup auto-upgrades)
• Deleted kubernetes/infra/cluster-issuers.yaml (self-signed issuer is now created by the metrics-server chart)
• Enhanced metrics-server.yaml with cert-manager TLS integration and dependency on cert-manager

Improved Health Checks

• Updated readiness expressions in apps.yaml and infra.yaml to check both Ready status and observedGeneration == metadata.generation

Bug Fixes

• Fixed scripts/flux-push.sh to reset diff_exit_code and push_exit_code variables between function calls (prevents false positives)
• Upgraded local registry from registry:2 to registry:3 in scripts/kind-up.sh

Documentation

• Updated README to remove Helm and add Flux Operator CLI to prerequisites
• Updated copyright year to 2025 in modified scripts