diff --git a/bootstrap/Makefile b/bootstrap/Makefile
index ad495bfd..5ba99d91 100644
--- a/bootstrap/Makefile
+++ b/bootstrap/Makefile
@@ -3,13 +3,8 @@
 
 KUBECONFIG = ../metal/kubeconfig.yaml
 
-default: argocd root
+default: argocd
 
 .PHONY: argocd
 argocd:
 	kustomize build ./argocd | kubectl apply -f -
-	# TODO wait for argocd
-
-.PHONY: root
-root:
-	kustomize build ./root | kubectl apply -f -
diff --git a/bootstrap/root/applicationsets/bootstrap.yaml b/bootstrap/argocd/bootstrap.yaml
similarity index 95%
rename from bootstrap/root/applicationsets/bootstrap.yaml
rename to bootstrap/argocd/bootstrap.yaml
index 01ae059b..41050177 100644
--- a/bootstrap/root/applicationsets/bootstrap.yaml
+++ b/bootstrap/argocd/bootstrap.yaml
@@ -21,5 +21,4 @@ spec:
         path: '{{path}}'
       syncPolicy:
         automated:
-          prune: true
           selfHeal: true
diff --git a/bootstrap/argocd/kustomization.yaml b/bootstrap/argocd/kustomization.yaml
index 245ace47..d52a1d64 100644
--- a/bootstrap/argocd/kustomization.yaml
+++ b/bootstrap/argocd/kustomization.yaml
@@ -6,6 +6,7 @@ resources:
 - https://raw.githubusercontent.com/argoproj/argo-cd/v2.2.0-rc1/manifests/install.yaml # TODO switch back to stable
 - https://raw.githubusercontent.com/argoproj-labs/applicationset/master/manifests/install.yaml # TODO switch back to stable
 - ingress.yaml
+- bootstrap.yaml
 
 patches:
 - path: argocd-server-deployment-patch.yaml
diff --git a/bootstrap/root/applicationsets/apps.yaml b/bootstrap/root/apps.yaml
similarity index 100%
rename from bootstrap/root/applicationsets/apps.yaml
rename to bootstrap/root/apps.yaml
diff --git a/bootstrap/root/kustomization.yaml b/bootstrap/root/kustomization.yaml
index fc1c199a..89e3d309 100644
--- a/bootstrap/root/kustomization.yaml
+++ b/bootstrap/root/kustomization.yaml
@@ -2,10 +2,8 @@ apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 
 resources:
-# - projects/system.yaml
-- applicationsets/bootstrap.yaml
-- applicationsets/system.yaml
-- applicationsets/platform.yaml
-- applicationsets/apps.yaml
+- system.yaml
+- platform.yaml
+- apps.yaml
 
 namespace: argocd
diff --git a/bootstrap/root/applicationsets/platform.yaml b/bootstrap/root/platform.yaml
similarity index 100%
rename from bootstrap/root/applicationsets/platform.yaml
rename to bootstrap/root/platform.yaml
diff --git a/bootstrap/root/projects/system.yaml b/bootstrap/root/projects/system.yaml
deleted file mode 100644
index d63e4b21..00000000
--- a/bootstrap/root/projects/system.yaml
+++ /dev/null
@@ -1,8 +0,0 @@
-apiVersion: argoproj.io/v1alpha1
-kind: AppProject
-metadata:
-  name: system
-spec:
-  description: System Project
-  sourceRepos:
-  - '*'
diff --git a/bootstrap/root/applicationsets/system.yaml b/bootstrap/root/system.yaml
similarity index 100%
rename from bootstrap/root/applicationsets/system.yaml
rename to bootstrap/root/system.yaml