diff --git a/apps/README.md b/apps/README.md
new file mode 100644
index 0000000..a7ef689
--- /dev/null
+++ b/apps/README.md
@@ -0,0 +1,27 @@
+# Apps
+This directory contains all of the applications you installed by using:
+```bash
+argocd-autopilot app create <APP_NAME> --app <APP_SPECIFIER> -p <PROJECT_NAME>
+```
+
+## Application Types
+> If you don't specify the application `--type` argocd-autopilot will try to clone the source repository and infer the application type [automatically](https://argoproj.github.io/argo-cd/user-guide/tool_detection/#tool-detection)
+
+* ### Directory application
+  Such an application references a specific directory at a given repo URL, path and revision. It will be persisted in the GitOps Repository as a single file at `apps/<APP_NAME>/<PROJECT_NAME>/config.json`.
+  #### Example:
+  ```bash
+  argocd-autopilot app create dir-example --app github.com/argoproj-labs/argocd-autopilot/examples/demo-dir/ -p <PROJECT_NAME> --type dir
+  ```
+
+* ### Kustomize application
+  A Kustomize application will have <u>exactly one</u>: `apps/<APP_NAME>/base/kustomization.yaml` file, and one or more `apps/<APP_NAME>/overlays/<PROJECT_NAME>/` folders.
+
+  The `apps/<APP_NAME>/base/kustomization.yaml` file is created the first time you create the application. The `apps/<APP_NAME>/overlays/<PROJECT_NAME>/` folder is created for each project you install this application on. So all overlays of the same application are using the same base `kustomization.yaml`.
+  #### Example:
+  Try running the following command:
+  ```bash
+  argocd-autopilot app create hello-world --app github.com/argoproj-labs/argocd-autopilot/examples/demo-app/ -p <PROJECT_NAME> --type kustomize
+  ```
+
+###### * If you did not create a project yet take a look at: [creating a project](https://argocd-autopilot.readthedocs.io/en/stable/Getting-Started/#add-a-project-and-an-application).
\ No newline at end of file
diff --git a/apps/my-app/base/kustomization.yaml b/apps/my-app/base/kustomization.yaml
new file mode 100644
index 0000000..233de2b
--- /dev/null
+++ b/apps/my-app/base/kustomization.yaml
@@ -0,0 +1,4 @@
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+resources:
+  - github.com/argoproj-labs/argocd-autopilot/examples/demo-app/
\ No newline at end of file
diff --git a/apps/my-app/overlays/k3s-cluster/config.json b/apps/my-app/overlays/k3s-cluster/config.json
new file mode 100644
index 0000000..f221d7c
--- /dev/null
+++ b/apps/my-app/overlays/k3s-cluster/config.json
@@ -0,0 +1,11 @@
+{
+  "appName": "my-app",
+  "userGivenName": "my-app",
+  "destNamespace": "default",
+  "destServer": "https://kubernetes.default.svc",
+  "srcPath": "apps/my-app/overlays/k3s-cluster",
+  "srcRepoURL": "https://github.com/3dwardch3ng/home-cluster-ops.git",
+  "srcTargetRevision": "",
+  "labels": null,
+  "annotations": null
+}
\ No newline at end of file
diff --git a/apps/my-app/overlays/k3s-cluster/kustomization.yaml b/apps/my-app/overlays/k3s-cluster/kustomization.yaml
new file mode 100644
index 0000000..a227ac4
--- /dev/null
+++ b/apps/my-app/overlays/k3s-cluster/kustomization.yaml
@@ -0,0 +1,4 @@
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+resources:
+  - ../../base
\ No newline at end of file
diff --git a/appsets/k3s-cluster-appset.yaml b/appsets/k3s-cluster-appset.yaml
deleted file mode 100644
index de6f7df..0000000
--- a/appsets/k3s-cluster-appset.yaml
+++ /dev/null
@@ -1,39 +0,0 @@
-apiVersion: argoproj.io/v1alpha1
-kind: ApplicationSet
-metadata:
-  name: k3s-cluster-appset
-  namespace: argocd
-spec:
-  goTemplate: true
-  goTemplateOptions: ["missingkey=error"]
-  generators:
-    - git:
-        repoURL: https://github.com/3dwardch3ng/home-cluster-ops.git
-        revision: HEAD
-        directories:
-          - path: apps/*/envs/k3s-cluster
-  template:
-    metadata:
-      name: '{{index .path.segments 1}}-{{index .path.segments 3}}'
-    spec:
-      # The project the application belongs to.
-      project: home-cluster-ops
-
-      # Source of the application manifests
-      source:
-        repoURL: https://github.com/3dwardch3ng/home-cluster-ops.git
-        targetRevision: HEAD
-        path: '{{.path.path}}'
-
-      # Destination cluster and namespace to deploy the application
-      destination:
-        server: https://kubernetes.default.svc
-        namespace: '{{index .path.segments 1}}-{{index .path.segments 3}}'
-
-      # Sync policy
-      syncPolicy:
-        syncOptions:
-          - CreateNamespace=true
-        automated: # automated sync by default retries failed attempts 5 times with following delays between attempts ( 5s, 10s, 20s, 40s, 80s ); retry controlled using `retry` field.
-          prune: true # Specifies if resources should be pruned during auto-syncing ( false by default ).
-          selfHeal: true # Specifies if partial app sync should be executed when resources are changed only in target Kubernetes cluster and no git change detected ( false by default ).
\ No newline at end of file
diff --git a/bootstrap/argo-cd.yaml b/bootstrap/argo-cd.yaml
new file mode 100644
index 0000000..a2e38bd
--- /dev/null
+++ b/bootstrap/argo-cd.yaml
@@ -0,0 +1,38 @@
+apiVersion: argoproj.io/v1alpha1
+kind: Application
+metadata:
+  creationTimestamp: null
+  labels:
+    app.kubernetes.io/managed-by: argocd-autopilot
+    app.kubernetes.io/name: argo-cd
+  name: argo-cd
+  namespace: argocd
+spec:
+  destination:
+    namespace: argocd
+    server: https://kubernetes.default.svc
+  ignoreDifferences:
+    - group: argoproj.io
+      jsonPointers:
+        - /status
+      kind: Application
+  project: default
+  source:
+    path: bootstrap/argo-cd
+    repoURL: https://github.com/3dwardch3ng/home-cluster-ops.git
+  syncPolicy:
+    automated:
+      allowEmpty: true
+      prune: true
+      selfHeal: true
+    syncOptions:
+      - allowEmpty=true
+status:
+  health: {}
+  summary: {}
+  sync:
+    comparedTo:
+      destination: {}
+      source:
+        repoURL: ""
+    status: ""
\ No newline at end of file
diff --git a/bootstrap/argo-cd/kustomization.yaml b/bootstrap/argo-cd/kustomization.yaml
new file mode 100644
index 0000000..6df5a48
--- /dev/null
+++ b/bootstrap/argo-cd/kustomization.yaml
@@ -0,0 +1,17 @@
+apiVersion: kustomize.config.k8s.io/v1beta1
+configMapGenerator:
+  - behavior: merge
+    literals:
+      - |
+        repository.credentials=- passwordSecret:
+            key: git_token
+            name: autopilot-secret
+          url: https://github.com/
+          usernameSecret:
+            key: git_username
+            name: autopilot-secret
+    name: argocd-cm
+kind: Kustomization
+namespace: argocd
+resources:
+  - github.com/argoproj-labs/argocd-autopilot/manifests/base?ref=v0.4.12
\ No newline at end of file
diff --git a/bootstrap/cluster-resources.yaml b/bootstrap/cluster-resources.yaml
new file mode 100644
index 0000000..4d93d10
--- /dev/null
+++ b/bootstrap/cluster-resources.yaml
@@ -0,0 +1,49 @@
+apiVersion: argoproj.io/v1alpha1
+kind: ApplicationSet
+metadata:
+  annotations:
+    argocd.argoproj.io/sync-wave: "0"
+  creationTimestamp: null
+  name: cluster-resources
+  namespace: argocd
+spec:
+  generators:
+    - git:
+        files:
+          - path: bootstrap/cluster-resources/*.json
+        repoURL: https://github.com/3dwardch3ng/home-cluster-ops.git
+        requeueAfterSeconds: 20
+        revision: ""
+        template:
+          metadata: {}
+          spec:
+            destination: {}
+            project: ""
+            source:
+              repoURL: ""
+  syncPolicy:
+    preserveResourcesOnDeletion: true
+  template:
+    metadata:
+      labels:
+        app.kubernetes.io/managed-by: argocd-autopilot
+        app.kubernetes.io/name: cluster-resources-{{name}}
+      name: cluster-resources-{{name}}
+      namespace: argocd
+    spec:
+      destination:
+        server: '{{server}}'
+      ignoreDifferences:
+        - group: argoproj.io
+          jsonPointers:
+            - /status
+          kind: Application
+      project: default
+      source:
+        path: bootstrap/cluster-resources/{{name}}
+        repoURL: https://github.com/3dwardch3ng/home-cluster-ops.git
+      syncPolicy:
+        automated:
+          allowEmpty: true
+          selfHeal: true
+status: {}
\ No newline at end of file
diff --git a/bootstrap/cluster-resources/in-cluster.json b/bootstrap/cluster-resources/in-cluster.json
new file mode 100644
index 0000000..259083a
--- /dev/null
+++ b/bootstrap/cluster-resources/in-cluster.json
@@ -0,0 +1 @@
+{"name":"in-cluster","server":"https://kubernetes.default.svc"}
\ No newline at end of file
diff --git a/bootstrap/cluster-resources/in-cluster/README.md b/bootstrap/cluster-resources/in-cluster/README.md
new file mode 100644
index 0000000..279f224
--- /dev/null
+++ b/bootstrap/cluster-resources/in-cluster/README.md
@@ -0,0 +1,3 @@
+# Cluster Resources
+This directory contains all cluster resources that should be applied to cluster: `in-cluster`.
+For example `Namespace` resources that are shared by multiple applications on the same namespace.
\ No newline at end of file
diff --git a/bootstrap/cluster-resources/in-cluster/argocd-ns.yaml b/bootstrap/cluster-resources/in-cluster/argocd-ns.yaml
new file mode 100644
index 0000000..b16706d
--- /dev/null
+++ b/bootstrap/cluster-resources/in-cluster/argocd-ns.yaml
@@ -0,0 +1,9 @@
+apiVersion: v1
+kind: Namespace
+metadata:
+  annotations:
+    argocd.argoproj.io/sync-options: Prune=false
+  creationTimestamp: null
+  name: argocd
+spec: {}
+status: {}
\ No newline at end of file
diff --git a/bootstrap/root.yaml b/bootstrap/root.yaml
new file mode 100644
index 0000000..a5802a6
--- /dev/null
+++ b/bootstrap/root.yaml
@@ -0,0 +1,40 @@
+apiVersion: argoproj.io/v1alpha1
+kind: Application
+metadata:
+  creationTimestamp: null
+  finalizers:
+    - resources-finalizer.argocd.argoproj.io
+  labels:
+    app.kubernetes.io/managed-by: argocd-autopilot
+    app.kubernetes.io/name: root
+  name: root
+  namespace: argocd
+spec:
+  destination:
+    namespace: argocd
+    server: https://kubernetes.default.svc
+  ignoreDifferences:
+    - group: argoproj.io
+      jsonPointers:
+        - /status
+      kind: Application
+  project: default
+  source:
+    path: projects
+    repoURL: https://github.com/3dwardch3ng/home-cluster-ops.git
+  syncPolicy:
+    automated:
+      allowEmpty: true
+      prune: true
+      selfHeal: true
+    syncOptions:
+      - allowEmpty=true
+status:
+  health: {}
+  summary: {}
+  sync:
+    comparedTo:
+      destination: {}
+      source:
+        repoURL: ""
+    status: ""
\ No newline at end of file
diff --git a/projects/k3s-cluster.yaml b/projects/k3s-cluster.yaml
new file mode 100644
index 0000000..4ec7b75
--- /dev/null
+++ b/projects/k3s-cluster.yaml
@@ -0,0 +1,94 @@
+apiVersion: argoproj.io/v1alpha1
+kind: AppProject
+metadata:
+  annotations:
+    argocd-autopilot.argoproj-labs.io/default-dest-server: https://kubernetes.default.svc
+    argocd.argoproj.io/sync-options: PruneLast=true
+    argocd.argoproj.io/sync-wave: "-2"
+  creationTimestamp: null
+  name: k3s-cluster
+  namespace: argocd
+spec:
+  clusterResourceWhitelist:
+    - group: '*'
+      kind: '*'
+  description: k3s-cluster project
+  destinations:
+    - namespace: '*'
+      server: '*'
+  namespaceResourceWhitelist:
+    - group: '*'
+      kind: '*'
+  sourceRepos:
+    - '*'
+status: {}
+---
+apiVersion: argoproj.io/v1alpha1
+kind: ApplicationSet
+metadata:
+  annotations:
+    argocd.argoproj.io/sync-wave: "0"
+  creationTimestamp: null
+  name: k3s-cluster
+  namespace: argocd
+spec:
+  generators:
+    - git:
+        files:
+          - path: apps/**/k3s-cluster/config.json
+        repoURL: V
+        requeueAfterSeconds: 20
+        revision: ""
+        template:
+          metadata: {}
+          spec:
+            destination: {}
+            project: ""
+            source:
+              repoURL: ""
+    - git:
+        files:
+          - path: apps/**/k3s-cluster/config_dir.json
+        repoURL: https://github.com/3dwardch3ng/home-cluster-ops.git
+        requeueAfterSeconds: 20
+        revision: ""
+        template:
+          metadata: {}
+          spec:
+            destination: {}
+            project: ""
+            source:
+              directory:
+                exclude: '{{ exclude }}'
+                include: '{{ include }}'
+                jsonnet: {}
+                recurse: true
+              repoURL: ""
+  syncPolicy: {}
+  template:
+    metadata:
+      labels:
+        app.kubernetes.io/managed-by: argocd-autopilot
+        app.kubernetes.io/name: '{{ appName }}'
+      name: k3s-cluster-{{ userGivenName }}
+      namespace: argocd
+    spec:
+      destination:
+        namespace: '{{ destNamespace }}'
+        server: '{{ destServer }}'
+      ignoreDifferences:
+        - group: argoproj.io
+          jsonPointers:
+            - /status
+          kind: Application
+      project: k3s-cluster
+      source:
+        path: '{{ srcPath }}'
+        repoURL: '{{ srcRepoURL }}'
+        targetRevision: '{{ srcTargetRevision }}'
+      syncPolicy:
+        automated:
+          allowEmpty: true
+          prune: true
+          selfHeal: true
+status: {}
\ No newline at end of file
diff --git a/root-argocd-app.yaml b/root-argocd-app.yaml
deleted file mode 100644
index 9432611..0000000
--- a/root-argocd-app.yaml
+++ /dev/null
@@ -1,20 +0,0 @@
-apiVersion: argoproj.io/v1alpha1
-kind: Application
-metadata:
-  name: all-apps
-  namespace: argocd
-spec:
-  project: home-cluster-ops
-  source:
-    repoURL: https://github.com/3dwardch3ng/home-cluster-ops.git
-    targetRevision: HEAD
-    path: appsets
-  destination:
-    server: https://kubernetes.default.svc
-    namespace: argocd
-  syncPolicy:
-    syncOptions:
-      - CreateNamespace=true
-    automated:
-      prune: true
-      selfHeal: true
\ No newline at end of file
diff --git a/scripts/3.bootstrap-argocd.sh b/scripts/3.bootstrap-argocd.sh
new file mode 100644
index 0000000..92d3a7a
--- /dev/null
+++ b/scripts/3.bootstrap-argocd.sh
@@ -0,0 +1,4 @@
+#!/bin/bash
+set -e
+
+argocd-autopilot repo bootstrap --app https://github.com/argoproj-labs/argocd-autopilot/manifests/ha
\ No newline at end of file