Flux GitOps Scaffold

Purpose

Scaffold and manage Flux CD GitOps repositories with:

• Multi-environment structure (dev/staging/prod)
• Infrastructure components (cert-manager, ingress-nginx, external-secrets)
• Application deployments with image automation
• External Secrets integration for secret management

Complementary to: helm-chart-developer skill (for Helm chart authoring). This skill focuses on GitOps project structure and Flux-specific patterns.

When to Use

Activate for:

• Creating new GitOps repositories from scratch
• Adding infrastructure components to existing GitOps projects
• Setting up application deployments with image automation
• Configuring Flux Kustomization dependencies
• Multi-environment deployment patterns

Project Structure Pattern

gitops/
├── clusters/{env}/              # Flux orchestration layer
│   ├── kustomization.yaml       # Aggregates all Flux Kustomizations
│   ├── 00-crds.yaml             # CRDs (prune: false, wait: true)
│   ├── 01-controllers.yaml      # dependsOn: crds
│   ├── 02-cluster-configs.yaml  # dependsOn: controllers
│   ├── 03-services.yaml         # dependsOn: cluster-configs
│   ├── 99-apps.yaml             # dependsOn: services, cluster-configs
│   └── flux-system/
│
├── infra/
│   ├── base/
│   │   ├── cluster/
│   │   │   ├── controllers/     # cert-manager, ingress-nginx, ESO
│   │   │   └── configs/         # ClusterIssuer, ClusterSecretStore
│   │   └── services/            # redis, postgres (with configs/secrets)
│   ├── crds/                    # Vendored CRDs (applied first)
│   │   ├── kustomization.yaml   # Aggregates all CRD subdirs
│   │   ├── cert-manager/
│   │   └── external-secrets/
│   └── {env}/
│       ├── cluster/
│       │   ├── controllers/     # values only (ConfigMapGenerator)
│       │   └── configs/         # plain manifests
│       └── services/            # values + configs + secrets
│
├── apps/
│   ├── base/{app}/              # Base HelmRelease
│   └── {env}/{app}/             # values + configs + secrets
│       ├── configs/             # Plain ConfigMaps
│       └── secrets/             # ExternalSecrets
│
└── charts/app/                  # Generic application chart

Structure Principle: Base + overlay with explicit layering. Controllers → Configs → Services → Apps.

See references/project-structure.md for detailed layout.

Core Workflows

1. Initialize GitOps Project

To create a new GitOps project:

1. Gather requirements via AskUserQuestion:

- Project name - Environments (dev, staging, prod) - Secrets provider (AWS/GCP/Azure/Vault) - Cloud region/project

1. Create directory structure per references/project-structure.md

1. Generate cluster orchestration files (numbered Kustomizations)

1. Copy generic Helm chart from assets/charts/app/

1. Fetch latest component versions via Context7

2. Add Infrastructure Component

Three workflows depending on component type:

2a. Add Controller (cert-manager, ingress-nginx, ESO)

1. FIRST: Get latest version via Context7 (see Version Management section)
2. Vendor CRDs to infra/crds/{component}/:

- kustomization.yaml - Resources reference - crds.yaml - Vendored from upstream (curl from release)

1. Create infra/base/cluster/controllers/{component}/:

- kustomization.yaml - Resources reference - helm.yaml - HelmRepository + HelmRelease (installCRDs: false)

1. Create infra/{env}/cluster/controllers/{component}/:

- kustomization.yaml - refs base + ConfigMapGenerator - values.yaml - Environment values (installCRDs: false)

1. Update infra/crds/kustomization.yaml aggregator
2. Update infra/{env}/cluster/controllers/kustomization.yaml aggregator

2b. Add Cluster Config (ClusterIssuer, ClusterSecretStore)

1. Create infra/base/cluster/configs/{component}/:

- kustomization.yaml - Resources reference - {component}.yaml - Plain manifest template

1. Create infra/{env}/cluster/configs/{component}/:

- kustomization.yaml - refs base - {component}.yaml - Environment-specific manifest

1. Update infra/{env}/cluster/configs/kustomization.yaml aggregator

2c. Add Service (redis, postgres)

1. FIRST: Get latest version via Context7 (see Version Management section)
2. Create infra/base/services/{component}/:

- kustomization.yaml - Resources reference - helm.yaml - HelmRepository + HelmRelease

1. Create infra/{env}/services/{component}/:

- kustomization.yaml - refs base + ConfigMapGenerator + configs + secrets - values.yaml - With envFrom injection - configs/{component}.config.yaml - Plain ConfigMap - secrets/{component}.external.yaml - ExternalSecret

1. Update infra/{env}/services/kustomization.yaml aggregator

Validation: Run kubectl kustomize infra/{env}/... to validate before commit.

See references/infra-components.md for supported components.

3. Add Application

To add application with image automation:

1. Gather via AskUserQuestion:

- Registry type (ECR/GCR/ACR/GHCR) - Image repository URL - Tag pattern (dev: run_id, prod: semver)

1. Create apps/base/{app}/:

- kustomization.yaml - Resources reference - helm.yaml - HelmRelease referencing charts/app

1. Create apps/{env}/{app}/:

- kustomization.yaml - refs base + ConfigMapGenerator + configs + secrets - values.yaml - With envFrom injection - patches.yaml - Image tag with automation marker - kustomizeconfig.yaml - ConfigMap name replacement - configs/{app}.config.yaml - Plain ConfigMap (non-sensitive) - secrets/{app}.external.yaml - ExternalSecret (sensitive)

1. Create image automation in apps/{env}/:

- image-automation.yaml - ImageRepository + ImagePolicy + ImageUpdateAutomation

1. Update apps/{env}/kustomization.yaml aggregator

See references/image-automation.md for registry-specific patterns.

API Versions

Always use these API versions:

CRITICAL: Never use deprecated versions (v2beta1, v2beta2). If found, propose migration.

Key Patterns

See [references/key-patterns.md](references/key-patterns.md) for detailed YAML patterns:

• HelmRelease with ConfigMap Values
• ConfigMap Generator (Kustomize overlay pattern)
• Flux Kustomization with Dependencies
• Image Automation Markers
• Configs & Secrets Pattern (ConfigMap, ExternalSecret, envFrom)

Orchestration

Five Flux Kustomizations with explicit dependsOn chain:

Why this order:

• CRDs must exist before controllers can install CRs
• Controllers must be running before configs (ClusterIssuer needs cert-manager)
• Cluster configs (ClusterSecretStore) needed before services can fetch secrets
• Services provide infrastructure for apps (redis, postgres)

Aggregator Pattern

Each directory Flux points to MUST have kustomization.yaml:

# infra/{env}/cluster/controllers/kustomization.yaml
apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization
resources:
  - cert-manager
  - ingress-nginx
  - external-secrets

CRD Management

CRITICAL: Vendor CRDs into repository. Do NOT use nested Flux Kustomizations for CRDs.

# Download vendored CRDs (use Context7 to get {VERSION} first!)
curl -sL https://github.com/cert-manager/cert-manager/releases/download/{VERSION}/cert-manager.crds.yaml \
  > infra/crds/cert-manager/crds.yaml

For HelmReleases with CRDs, disable CRD installation:

# values.yaml
installCRDs: false

Version Management (MANDATORY)

CRITICAL: Never hardcode versions. Always use Context7 to get current versions.

Enforcement Layers

1. SessionStart hook — Reminds about Context7 when k8s/Flux project detected
2. PreToolUse hook — Checks versions in HelmRelease files:

- Empty version (version: "") → Blocks and requires Context7 - Hardcoded version (version: "1.2.3") → Asks for verification

1. Documentation — No hardcoded versions provided (only Context7 workflow)

Workflow (REQUIRED for every HelmRelease)

Before creating ANY HelmRelease or vendoring CRDs:

# Step 1: Resolve library ID
Tool: resolve-library-id
Parameter: libraryName="{component}"

# Step 2: Query docs for version
Tool: query-docs
Parameters:
  libraryId: "/{org}/{project}"
  topic: "helm chart installation version"

# Step 3: Use version from documentation

Example: cert-manager

Tool: resolve-library-id
libraryName: "cert-manager"
# Returns: /jetstack/cert-manager

Tool: query-docs
libraryId: "/jetstack/cert-manager"
topic: "helm installation version"
# Extract version from documentation

Guardrails

NEVER:

• Copy versions from examples or documentation files
• Use versions from memory or previous sessions
• Hardcode versions without Context7 verification

ALWAYS:

• Fetch version via Context7 for EVERY new HelmRelease
• Verify version is current before deployment
• Use empty version: "" as placeholder until Context7 fetched

See references/version-matrix.md for Context7 library IDs per component.

Validation

Before committing GitOps manifests, validate structure with kubectl kustomize:

# Validate infra component
kubectl kustomize infra/dev/cert-manager

# Validate apps
kubectl kustomize apps/dev

# Validate entire environment (from cluster kustomization)
kubectl kustomize clusters/dev

This catches:

• Missing files referenced in kustomization.yaml
• Invalid patches
• YAML syntax errors
• Invalid resource references

Definition of Done

Before completing GitOps scaffolding:

1. Structure: All directories created per pattern
2. Validation: kubectl kustomize passes for all directories
3. Dependencies: dependsOn set correctly in Kustomizations
4. Versions: Latest versions fetched via Context7
5. API Versions: All using current stable APIs
6. Values: ConfigMapGenerator with disableNameSuffixHash: true
7. Secrets: ExternalSecret configured (not hardcoded secrets)
8. Image Automation: Markers set for automated updates

Anti-Patterns

Examples

Trigger phrases:

• "Create a new GitOps repository for my microservices"
• "Add cert-manager to my Flux project"
• "Set up image automation for my app"
• "Configure multi-environment deployment"
• "Add ingress-nginx infrastructure"
• "Set up External Secrets with AWS"

Additional Resources

Reference Files

For detailed patterns, consult:

• references/project-structure.md - Full directory layout
• references/image-automation.md - Registry-specific automation
• references/infra-components.md - Infrastructure patterns
• references/version-matrix.md - Current versions + Context7 usage

Example Files

Working examples in examples/:

Orchestration:

• orchestration-kustomizations.yaml - All 5 Flux Kustomizations with dependsOn chain

Controllers & Configs:

• infra-base-helm.yaml - Base HelmRepo + HelmRelease for controller
• cluster-controller-overlay.yaml - Controller overlay (values only)
• cluster-config-overlay.yaml - Cluster config overlay (ClusterIssuer)

Services & Apps (with configs/secrets):

• service-overlay-full.yaml - Service with configs/secrets
• app-overlay-full.yaml - App with configs/secrets
• config-configmap.yaml - Plain ConfigMap pattern
• values-with-envfrom.yaml - values.yaml with envFrom injection

CRDs & Image Automation:

• crds-kustomization.yaml - Vendored CRDs aggregator
• image-automation-ecr.yaml - ECR automation
• image-automation-ghcr.yaml - GHCR automation
• external-secret.yaml - ESO pattern

Assets

Generic chart template in assets/charts/app/ - copy to target project.

Related Skills

• helm-chart-developer - Helm chart authoring and ESO integration
• conventional-commit - Commit message formatting