feat: add ArgoCD bootstrap with ApplicationSet pattern

- Add root ApplicationSet using Git Directory Generator
- Configure AppProjects for infrastructure and apps separation
- Add cert-manager with Let's Encrypt ClusterIssuers (staging/prod)
- Add SOPS configuration for age-encrypted secrets
- Add bootstrap documentation (docs/BOOTSTRAP.md)
- Scaffold infrastructure dirs (networking, storage, monitoring)
- Update README with quick start and architecture

GitOps pattern: directories auto-discovered by ArgoCD ApplicationSets
Reference: CNCF App-of-Apps best practices 2025

.sops.yaml

@@ -0,0 +1,31 @@
+# .sops.yaml
+# SOPS configuration for encrypting Kubernetes secrets
+# Generate age key: age-keygen -o key.txt
+# Export: export SOPS_AGE_KEY_FILE=~/.config/sops/age/keys.txt
+# Encrypt: sops -e -i secret.yaml
+# Decrypt: sops -d secret.yaml
+#
+# Reference: https://github.com/getsops/sops
+
+creation_rules:
+  # Infrastructure secrets (networking, storage, monitoring)
+  - path_regex: infrastructure/.*/.*secret.*\.yaml$
+    encrypted_regex: ^(data|stringData)$
+    age: >-
+      age1xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+
+  # Application secrets
+  - path_regex: apps/.*/.*secret.*\.yaml$
+    encrypted_regex: ^(data|stringData)$
+    age: >-
+      age1xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+
+  # Cluster-specific secrets
+  - path_regex: clusters/.*/.*secret.*\.yaml$
+    encrypted_regex: ^(data|stringData)$
+    age: >-
+      age1xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+
+# NOTE: Replace the age public key above with your actual key
+# The encrypted_regex ensures only data/stringData fields are encrypted,
+# leaving metadata readable for GitOps tooling

README.md

@@ -1,10 +1,20 @@
 # Homelab GitOps
 
 ![Kubernetes](https://img.shields.io/badge/k3s-1.28+-326CE5?style=flat&logo=kubernetes&logoColor=white)
-![ArgoCD](https://img.shields.io/badge/GitOps-Ready-EF7B4D?style=flat&logo=argo&logoColor=white)
+![ArgoCD](https://img.shields.io/badge/ArgoCD-2.10+-EF7B4D?style=flat&logo=argo&logoColor=white)
+![SOPS](https://img.shields.io/badge/SOPS-age-green?style=flat)
 ![License](https://img.shields.io/badge/License-MIT-blue)
 
-GitOps repository for homelab Kubernetes infrastructure. Everything as code.
+GitOps repository for homelab Kubernetes infrastructure. Everything as code, auto-synced by ArgoCD.
+
+## Quick Start
+
+```bash
+# Bootstrap cluster (after ArgoCD installed)
+kubectl apply -k clusters/defiant/
+```
+
+See [docs/BOOTSTRAP.md](docs/BOOTSTRAP.md) for full setup guide.
 
 ## Infrastructure
 
@@ -18,16 +28,32 @@ GitOps repository for homelab Kubernetes infrastructure. Everything as code.
 
 ```
 ├── apps/                    # Application deployments
-│   ├── base/            # Base manifests
+│   ├── base/               # Base manifests (Kustomize)
 │   └── overlays/           # Environment overrides
+│       ├── prod/           # → Auto-discovered by ApplicationSet
+│       └── dev/
 ├── infrastructure/          # Cluster infrastructure
-│   ├── networking/      # Ingress, certs, DNS
+│   ├── cert-manager/       # ✅ TLS with Let's Encrypt
-│   ├── storage/         # NFS, PVCs
+│   ├── networking/         # Istio gateway, NetworkPolicies
-│   └── monitoring/      # Prometheus, Grafana
+│   ├── storage/            # NFS StorageClass
-└── clusters/
+│   └── monitoring/         # Prometheus, Grafana, Loki
-    └── defiant/         # k3s cluster config
+├── clusters/
+│   └── defiant/            # Cluster bootstrap
+│       ├── kustomization.yaml
+│       ├── root-applicationset.yaml  # Git Directory Generator
+│       └── projects.yaml   # ArgoCD AppProjects
+└── docs/
+    └── BOOTSTRAP.md        # Setup guide
 ```
 
+## GitOps Pattern
+
+Uses **ArgoCD ApplicationSets** with Git Directory Generator:
+
+- `infrastructure/*` → Auto-creates ArgoCD Applications
+- `apps/overlays/prod/*` → Auto-creates prod Applications
+- Add a directory, push, ArgoCD syncs automatically
+
 ## Defiant (k3s) Workloads
 
 - 🏥 MediSynth - FHIR healthcare platform
@@ -43,9 +69,17 @@ GitOps repository for homelab Kubernetes infrastructure. Everything as code.
 - 🏠 Home Assistant
 - 📊 Homepage, Uptime Kuma
 
-## Secrets
+## Secrets Management
 
-Encrypted with SOPS + age. Never committed in plain text.
+Encrypted with **SOPS + age**. Configuration in `.sops.yaml`.
+
+```bash
+# Encrypt a secret
+sops -e -i infrastructure/cert-manager/secret.yaml
+
+# Decrypt for editing
+sops infrastructure/cert-manager/secret.yaml
+```
 
 ## License
 

apps/base/.gitkeep

@@ -0,0 +1,2 @@
+# Base manifests for applications
+# Use Kustomize bases here, overlays in apps/overlays/{env}/

apps/overlays/dev/.gitkeep

@@ -0,0 +1,2 @@
+# Development overlay directory
+# Add dev-specific patches and configurations here

apps/overlays/prod/.gitkeep

@@ -0,0 +1,2 @@
+# Production overlay directory
+# Each subdirectory here becomes an ArgoCD Application via ApplicationSet

clusters/defiant/argocd-namespace.yaml

@@ -0,0 +1,12 @@
+# clusters/defiant/argocd-namespace.yaml
+# ArgoCD namespace with required labels
+apiVersion: v1
+kind: Namespace
+metadata:
+  name: argocd
+  labels:
+    app.kubernetes.io/name: argocd
+    app.kubernetes.io/part-of: argocd
+    # Pod Security Standards - privileged for ArgoCD repo-server
+    pod-security.kubernetes.io/enforce: baseline
+    pod-security.kubernetes.io/warn: restricted

clusters/defiant/kustomization.yaml

@@ -0,0 +1,12 @@
+# clusters/defiant/kustomization.yaml
+# Root Kustomization for defiant k3s cluster
+# Applied by ArgoCD or manually via: kubectl apply -k clusters/defiant/
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+
+namespace: argocd
+
+resources:
+  - argocd-namespace.yaml
+  - root-applicationset.yaml
+  - projects.yaml

clusters/defiant/projects.yaml

@@ -0,0 +1,49 @@
+# clusters/defiant/projects.yaml
+# ArgoCD AppProjects for access control and grouping
+---
+apiVersion: argoproj.io/v1alpha1
+kind: AppProject
+metadata:
+  name: infrastructure
+  namespace: argocd
+  finalizers:
+    - resources-finalizer.argocd.argoproj.io
+spec:
+  description: Core cluster infrastructure (networking, storage, monitoring)
+  sourceRepos:
+    - 'https://github.com/ghndrx/homelab-gitops.git'
+    - 'https://charts.jetstack.io'
+    - 'https://prometheus-community.github.io/helm-charts'
+    - 'https://grafana.github.io/helm-charts'
+  destinations:
+    - namespace: '*'
+      server: https://kubernetes.default.svc
+  clusterResourceWhitelist:
+    - group: '*'
+      kind: '*'
+  namespaceResourceWhitelist:
+    - group: '*'
+      kind: '*'
+---
+apiVersion: argoproj.io/v1alpha1
+kind: AppProject
+metadata:
+  name: apps
+  namespace: argocd
+  finalizers:
+    - resources-finalizer.argocd.argoproj.io
+spec:
+  description: User-facing applications
+  sourceRepos:
+    - 'https://github.com/ghndrx/homelab-gitops.git'
+  destinations:
+    - namespace: 'prod-*'
+      server: https://kubernetes.default.svc
+    - namespace: 'dev-*'
+      server: https://kubernetes.default.svc
+  clusterResourceWhitelist:
+    - group: ''
+      kind: Namespace
+  namespaceResourceWhitelist:
+    - group: '*'
+      kind: '*'

clusters/defiant/root-applicationset.yaml

@@ -0,0 +1,96 @@
+# clusters/defiant/root-applicationset.yaml
+# Root ApplicationSet using Git Directory Generator
+# Automatically creates ArgoCD Applications for each component in infrastructure/
+# Reference: https://argo-cd.readthedocs.io/en/latest/operator-manual/applicationset/Generators-Git/
+---
+apiVersion: argoproj.io/v1alpha1
+kind: ApplicationSet
+metadata:
+  name: infrastructure
+  namespace: argocd
+spec:
+  goTemplate: true
+  goTemplateOptions: ["missingkey=error"]
+  generators:
+    - git:
+        repoURL: https://github.com/ghndrx/homelab-gitops.git
+        revision: HEAD
+        directories:
+          - path: infrastructure/*
+  template:
+    metadata:
+      name: '{{ .path.basename }}'
+      namespace: argocd
+      labels:
+        app.kubernetes.io/part-of: homelab-infrastructure
+      finalizers:
+        - resources-finalizer.argocd.argoproj.io
+    spec:
+      project: infrastructure
+      source:
+        repoURL: https://github.com/ghndrx/homelab-gitops.git
+        targetRevision: HEAD
+        path: '{{ .path.path }}'
+      destination:
+        server: https://kubernetes.default.svc
+        namespace: '{{ .path.basename }}'
+      syncPolicy:
+        automated:
+          prune: true
+          selfHeal: true
+          allowEmpty: false
+        syncOptions:
+          - CreateNamespace=true
+          - PrunePropagationPolicy=foreground
+          - PruneLast=true
+        retry:
+          limit: 5
+          backoff:
+            duration: 5s
+            factor: 2
+            maxDuration: 3m
+---
+apiVersion: argoproj.io/v1alpha1
+kind: ApplicationSet
+metadata:
+  name: apps
+  namespace: argocd
+spec:
+  goTemplate: true
+  goTemplateOptions: ["missingkey=error"]
+  generators:
+    - git:
+        repoURL: https://github.com/ghndrx/homelab-gitops.git
+        revision: HEAD
+        directories:
+          - path: apps/overlays/prod/*
+  template:
+    metadata:
+      name: 'prod-{{ .path.basename }}'
+      namespace: argocd
+      labels:
+        app.kubernetes.io/part-of: homelab-apps
+        environment: prod
+      finalizers:
+        - resources-finalizer.argocd.argoproj.io
+    spec:
+      project: apps
+      source:
+        repoURL: https://github.com/ghndrx/homelab-gitops.git
+        targetRevision: HEAD
+        path: '{{ .path.path }}'
+      destination:
+        server: https://kubernetes.default.svc
+        namespace: 'prod-{{ .path.basename }}'
+      syncPolicy:
+        automated:
+          prune: true
+          selfHeal: true
+        syncOptions:
+          - CreateNamespace=true
+        retry:
+          limit: 3
+          backoff:
+            duration: 5s
+            factor: 2
+            maxDuration: 1m

docs/BOOTSTRAP.md

@@ -0,0 +1,102 @@
+# Cluster Bootstrap Guide
+
+This guide walks through bootstrapping a new k3s cluster with ArgoCD GitOps.
+
+## Prerequisites
+
+- k3s cluster running
+- `kubectl` configured with cluster access
+- `age` installed for SOPS encryption
+- GitHub repo access configured
+
+## 1. Install ArgoCD
+
+```bash
+# Create namespace
+kubectl create namespace argocd
+
+# Install ArgoCD
+kubectl apply -n argocd -f https://raw.githubusercontent.com/argoproj/argo-cd/stable/manifests/install.yaml
+
+# Wait for pods
+kubectl wait --for=condition=available deployment/argocd-server -n argocd --timeout=300s
+```
+
+## 2. Configure SOPS
+
+```bash
+# Generate age key (one-time)
+age-keygen -o ~/.config/sops/age/keys.txt
+
+# Get public key
+cat ~/.config/sops/age/keys.txt | grep "public key"
+
+# Update .sops.yaml with your public key
+# Create k8s secret for ArgoCD to decrypt
+kubectl create secret generic sops-age \
+  --namespace=argocd \
+  --from-file=key.txt=~/.config/sops/age/keys.txt
+```
+
+## 3. Bootstrap the Cluster
+
+```bash
+# Apply root kustomization
+kubectl apply -k clusters/defiant/
+
+# This creates:
+# - ArgoCD namespace with PSS labels
+# - AppProjects (infrastructure, apps)
+# - Root ApplicationSets that auto-discover components
+```
+
+## 4. Access ArgoCD UI
+
+```bash
+# Get initial admin password
+kubectl -n argocd get secret argocd-initial-admin-secret \
+  -o jsonpath="{.data.password}" | base64 -d
+
+# Port forward
+kubectl port-forward svc/argocd-server -n argocd 8080:443
+
+# Open https://localhost:8080
+# Username: admin
+```
+
+## 5. Verify Infrastructure
+
+After bootstrap, ArgoCD will automatically sync:
+
+- **cert-manager** - TLS certificate management with Let's Encrypt
+- **networking** - Istio gateway (when configured)
+- **storage** - NFS StorageClass (when configured)
+- **monitoring** - Prometheus/Grafana (when configured)
+
+## Adding New Infrastructure
+
+1. Create directory under `infrastructure/<component>/`
+2. Add `kustomization.yaml` (required)
+3. Add manifests or helmCharts
+4. Commit and push
+5. ArgoCD auto-discovers via Git Directory Generator
+
+## Adding Applications
+
+1. Create base in `apps/base/<app>/`
+2. Create overlay in `apps/overlays/prod/<app>/`
+3. Commit and push
+4. ArgoCD creates Application automatically
+
+## Troubleshooting
+
+```bash
+# Check ApplicationSet status
+kubectl get applicationsets -n argocd
+
+# Check Application sync status
+kubectl get applications -n argocd
+
+# View ArgoCD logs
+kubectl logs -n argocd deployment/argocd-applicationset-controller
+```

infrastructure/cert-manager/clusterissuers.yaml

@@ -0,0 +1,54 @@
+# infrastructure/cert-manager/clusterissuers.yaml
+# Let's Encrypt ClusterIssuers for TLS certificates
+# Usage: Add annotation to Ingress:
+#   cert-manager.io/cluster-issuer: letsencrypt-prod
+---
+apiVersion: cert-manager.io/v1
+kind: ClusterIssuer
+metadata:
+  name: letsencrypt-staging
+spec:
+  acme:
+    # Staging endpoint for testing (higher rate limits, fake certs)
+    server: https://acme-staging-v02.api.letsencrypt.org/directory
+    email: admin@example.com  # TODO: Update with your email
+    privateKeySecretRef:
+      name: letsencrypt-staging-account-key
+    solvers:
+      # HTTP-01 challenge via Ingress
+      - http01:
+          ingress:
+            ingressClassName: istio
+---
+apiVersion: cert-manager.io/v1
+kind: ClusterIssuer
+metadata:
+  name: letsencrypt-prod
+spec:
+  acme:
+    # Production endpoint (rate limited, real certs)
+    server: https://acme-v02.api.letsencrypt.org/directory
+    email: admin@example.com  # TODO: Update with your email
+    privateKeySecretRef:
+      name: letsencrypt-prod-account-key
+    solvers:
+      # HTTP-01 challenge via Ingress
+      - http01:
+          ingress:
+            ingressClassName: istio
+---
+apiVersion: cert-manager.io/v1
+kind: ClusterIssuer
+metadata:
+  name: selfsigned
+spec:
+  selfSigned: {}
+---
+# Internal CA for service-to-service mTLS
+apiVersion: cert-manager.io/v1
+kind: ClusterIssuer
+metadata:
+  name: internal-ca
+spec:
+  ca:
+    secretName: internal-ca-key-pair

infrastructure/cert-manager/kustomization.yaml

@@ -0,0 +1,48 @@
+# infrastructure/cert-manager/kustomization.yaml
+# Cert-Manager with Let's Encrypt ClusterIssuers
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+
+namespace: cert-manager
+
+resources:
+  - namespace.yaml
+  - clusterissuers.yaml
+
+helmCharts:
+  - name: cert-manager
+    repo: https://charts.jetstack.io
+    version: v1.14.4
+    releaseName: cert-manager
+    namespace: cert-manager
+    valuesInline:
+      installCRDs: true
+      replicaCount: 1
+      # Pod Security Standards compliance
+      podSecurityPolicy:
+        enabled: false
+      securityContext:
+        runAsNonRoot: true
+        seccompProfile:
+          type: RuntimeDefault
+      containerSecurityContext:
+        allowPrivilegeEscalation: false
+        capabilities:
+          drop:
+            - ALL
+        readOnlyRootFilesystem: true
+      webhook:
+        securityContext:
+          runAsNonRoot: true
+          seccompProfile:
+            type: RuntimeDefault
+      cainjector:
+        securityContext:
+          runAsNonRoot: true
+          seccompProfile:
+            type: RuntimeDefault
+      # Prometheus ServiceMonitor
+      prometheus:
+        enabled: true
+        servicemonitor:
+          enabled: true

infrastructure/cert-manager/namespace.yaml

@@ -0,0 +1,11 @@
+# infrastructure/cert-manager/namespace.yaml
+apiVersion: v1
+kind: Namespace
+metadata:
+  name: cert-manager
+  labels:
+    app.kubernetes.io/name: cert-manager
+    app.kubernetes.io/component: certificate-management
+    # Pod Security Standards
+    pod-security.kubernetes.io/enforce: restricted
+    pod-security.kubernetes.io/warn: restricted

infrastructure/monitoring/kustomization.yaml

@@ -0,0 +1,13 @@
+# infrastructure/monitoring/kustomization.yaml
+# Monitoring: Prometheus, Grafana, Alertmanager
+# TODO: Add kube-prometheus-stack helm chart
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+
+namespace: monitoring
+
+resources: []
+# Future additions via helmCharts:
+# - kube-prometheus-stack
+# - loki
+# - grafana dashboards

infrastructure/networking/kustomization.yaml

@@ -0,0 +1,12 @@
+# infrastructure/networking/kustomization.yaml
+# Networking stack: Istio ingress, DNS, Network Policies
+# TODO: Add Istio Gateway, VirtualService templates
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+
+namespace: istio-system
+
+resources: []
+# Future additions:
+# - gateway.yaml
+# - default-network-policies.yaml

infrastructure/storage/kustomization.yaml

@@ -0,0 +1,10 @@
+# infrastructure/storage/kustomization.yaml
+# Storage: NFS provisioner, PVC templates
+# TODO: Add NFS StorageClass pointing to TrueNAS
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+
+resources: []
+# Future additions:
+# - nfs-storageclass.yaml
+# - default-pvc-templates.yaml