diff --git a/cmd/document/document_test.go b/cmd/document/document_test.go
index db910d00e..8f5e764b7 100644
--- a/cmd/document/document_test.go
+++ b/cmd/document/document_test.go
@@ -33,11 +33,6 @@ func TestDocument(t *testing.T) {
 			CmdLine: "-h",
 			Cmd:     document.NewPluginCommand(),
 		},
-		{
-			Name:    "document-pull-with-help",
-			CmdLine: "-h",
-			Cmd:     document.NewPullCommand(nil),
-		},
 	}
 	for _, tt := range tests {
 		testutil.RunTest(t, tt)
diff --git a/cmd/document/pull.go b/cmd/document/pull.go
index b3faa3a9b..38d392035 100644
--- a/cmd/document/pull.go
+++ b/cmd/document/pull.go
@@ -23,13 +23,17 @@ import (
 
 // NewPullCommand creates a new command for pulling airship document repositories
 func NewPullCommand(cfgFactory config.Factory) *cobra.Command {
+	var noCheckout bool
 	documentPullCmd := &cobra.Command{
 		Use:   "pull",
 		Short: "Pulls documents from remote git repository",
 		RunE: func(cmd *cobra.Command, args []string) error {
-			return pull.Pull(cfgFactory)
+			return pull.Pull(cfgFactory, noCheckout)
 		},
 	}
 
+	documentPullCmd.Flags().BoolVarP(&noCheckout, "no-checkout", "n", false,
+		"No checkout is performed after the clone is complete.")
+
 	return documentPullCmd
 }
diff --git a/cmd/document/testdata/TestDocumentGoldenOutput/document-pull-with-help.golden b/cmd/document/testdata/TestDocumentGoldenOutput/document-pull-with-help.golden
deleted file mode 100644
index b618d9ded..000000000
--- a/cmd/document/testdata/TestDocumentGoldenOutput/document-pull-with-help.golden
+++ /dev/null
@@ -1,7 +0,0 @@
-Pulls documents from remote git repository
-
-Usage:
-  pull [flags]
-
-Flags:
-  -h, --help   help for pull
diff --git a/cmd/document/testdata/TestPullGoldenOutput/document-pull-cmd-with-help.golden b/cmd/document/testdata/TestPullGoldenOutput/document-pull-cmd-with-help.golden
index b618d9ded..d2e2c889c 100644
--- a/cmd/document/testdata/TestPullGoldenOutput/document-pull-cmd-with-help.golden
+++ b/cmd/document/testdata/TestPullGoldenOutput/document-pull-cmd-with-help.golden
@@ -4,4 +4,5 @@ Usage:
   pull [flags]
 
 Flags:
-  -h, --help   help for pull
+  -h, --help          help for pull
+  -n, --no-checkout   No checkout is performed after the clone is complete.
diff --git a/docs/source/cli/airshipctl_document_pull.md b/docs/source/cli/airshipctl_document_pull.md
index 086c240e4..71e6894d4 100644
--- a/docs/source/cli/airshipctl_document_pull.md
+++ b/docs/source/cli/airshipctl_document_pull.md
@@ -13,7 +13,8 @@ airshipctl document pull [flags]
 ### Options
 
 ```
-  -h, --help   help for pull
+  -h, --help          help for pull
+  -n, --no-checkout   No checkout is performed after the clone is complete.
 ```
 
 ### Options inherited from parent commands
diff --git a/manifests/function/clusterctl/clusterctl.yaml b/manifests/function/clusterctl/clusterctl.yaml
index 766e53aaf..7380053a3 100644
--- a/manifests/function/clusterctl/clusterctl.yaml
+++ b/manifests/function/clusterctl/clusterctl.yaml
@@ -3,7 +3,7 @@ kind: Clusterctl
 metadata:
   labels:
     airshipit.org/deploy-k8s: "false"
-  name: clusterctl-v1
+  name: clusterctl_init
 init-options:
   core-provider: "cluster-api:v0.3.7"
   bootstrap-providers:
@@ -17,22 +17,22 @@ providers:
     type: "InfrastructureProvider"
     variable-substitution: true
     versions:
-      v0.3.2: manifests/function/capm3/v0.3.2
+      v0.3.2: airshipctl/manifests/function/capm3/v0.3.2
   - name: "kubeadm"
     type: "BootstrapProvider"
     variable-substitution: true
     versions:
-      v0.3.7: manifests/function/cabpk/v0.3.7
+      v0.3.7: airshipctl/manifests/function/cabpk/v0.3.7
   - name: "cluster-api"
     type: "CoreProvider"
     variable-substitution: true
     versions:
-      v0.3.7: manifests/function/capi/v0.3.7
+      v0.3.7: airshipctl/manifests/function/capi/v0.3.7
   - name: "kubeadm"
     type: "ControlPlaneProvider"
     variable-substitution: true
     versions:
-      v0.3.7: manifests/function/cacpk/v0.3.7
+      v0.3.7: airshipctl/manifests/function/cacpk/v0.3.7
 # These default images can be overridden via the `replacements/` entrypoint
 additional-vars:
   CONTAINER_CAPM3_MANAGER: quay.io/metal3-io/cluster-api-provider-metal3:v0.3.2
diff --git a/manifests/metadata.yaml b/manifests/metadata.yaml
index c57a228f3..b4fbe8880 100644
--- a/manifests/metadata.yaml
+++ b/manifests/metadata.yaml
@@ -1,2 +1,2 @@
 phase:
-  path: manifests/phases
\ No newline at end of file
+  path: airshipctl/manifests/phases
\ No newline at end of file
diff --git a/manifests/phases/clusterctl_init_options.yaml b/manifests/phases/clusterctl_init_options.yaml
new file mode 100755
index 000000000..3759b3685
--- /dev/null
+++ b/manifests/phases/clusterctl_init_options.yaml
@@ -0,0 +1,6 @@
+---
+apiVersion: airshipit.org/v1alpha1
+kind: Clusterctl
+metadata:
+  name: clusterctl_init
+action: init
diff --git a/manifests/phases/executors.yaml b/manifests/phases/executors.yaml
index 5078823c8..6a9f720e1 100644
--- a/manifests/phases/executors.yaml
+++ b/manifests/phases/executors.yaml
@@ -19,53 +19,6 @@ move-options: {}
 action: move
 ---
 apiVersion: airshipit.org/v1alpha1
-kind: Clusterctl
-metadata:
-  labels:
-    airshipit.org/deploy-k8s: "false"
-  name: clusterctl_init
-init-options:
-  core-provider: "cluster-api:v0.3.7"
-  bootstrap-providers:
-    - "kubeadm:v0.3.7"
-  infrastructure-providers:
-    - "metal3:v0.3.2"
-  control-plane-providers:
-    - "kubeadm:v0.3.7"
-action: init
-providers:
-  - name: "metal3"
-    type: "InfrastructureProvider"
-    variable-substitution: true
-    versions:
-      v0.3.2: manifests/function/capm3/v0.3.2
-  - name: "kubeadm"
-    type: "BootstrapProvider"
-    variable-substitution: true
-    versions:
-      v0.3.7: manifests/function/cabpk/v0.3.7
-  - name: "cluster-api"
-    type: "CoreProvider"
-    variable-substitution: true
-    versions:
-      v0.3.7: manifests/function/capi/v0.3.7
-  - name: "kubeadm"
-    type: "ControlPlaneProvider"
-    variable-substitution: true
-    versions:
-      v0.3.7: manifests/function/cacpk/v0.3.7
-# These default images can be overridden via the `replacements/` entrypoint
-additional-vars:
-  CONTAINER_CAPM3_MANAGER: quay.io/metal3-io/cluster-api-provider-metal3:v0.3.2
-  CONTAINER_CACPK_MANAGER: us.gcr.io/k8s-artifacts-prod/cluster-api/kubeadm-control-plane-controller:v0.3.7
-  CONTAINER_CABPK_MANAGER: us.gcr.io/k8s-artifacts-prod/cluster-api/kubeadm-bootstrap-controller:v0.3.7
-  CONTAINER_CAPI_MANAGER:  us.gcr.io/k8s-artifacts-prod/cluster-api/cluster-api-controller:v0.3.7
-  CONTAINER_CAPM3_AUTH_PROXY: gcr.io/kubebuilder/kube-rbac-proxy:v0.4.0
-  CONTAINER_CACPK_AUTH_PROXY: gcr.io/kubebuilder/kube-rbac-proxy:v0.4.1
-  CONTAINER_CABPK_AUTH_PROXY: gcr.io/kubebuilder/kube-rbac-proxy:v0.4.1
-  CONTAINER_CAPI_AUTH_PROXY: gcr.io/kubebuilder/kube-rbac-proxy:v0.4.1
----
-apiVersion: airshipit.org/v1alpha1
 kind: ImageConfiguration
 metadata:
   name: isogen
diff --git a/manifests/phases/kustomization.yaml b/manifests/phases/kustomization.yaml
index 058e38fd2..bb5cb9adb 100644
--- a/manifests/phases/kustomization.yaml
+++ b/manifests/phases/kustomization.yaml
@@ -3,4 +3,7 @@ resources:
   - plan.yaml
   - executors.yaml
   - cluster-map.yaml
-  - kubeconfig.yaml
\ No newline at end of file
+  - kubeconfig.yaml
+  - ../function/clusterctl
+patchesStrategicMerge:
+  - clusterctl_init_options.yaml
diff --git a/manifests/phases/phases.yaml b/manifests/phases/phases.yaml
index a97c6e329..2f41f38e0 100644
--- a/manifests/phases/phases.yaml
+++ b/manifests/phases/phases.yaml
@@ -7,7 +7,7 @@ config:
     apiVersion: airshipit.org/v1alpha1
     kind: ImageConfiguration
     name: isogen
-  documentEntryPoint: manifests/site/test-site/ephemeral/bootstrap
+  documentEntryPoint: airshipctl/manifests/site/test-site/ephemeral/bootstrap
 ---
 apiVersion: airshipit.org/v1alpha1
 kind: Phase
@@ -19,7 +19,7 @@ config:
     apiVersion: airshipit.org/v1alpha1
     kind: KubernetesApply
     name: kubernetes-apply
-  documentEntryPoint: manifests/site/test-site/ephemeral/initinfra
+  documentEntryPoint: airshipctl/manifests/site/test-site/ephemeral/initinfra
 ---
 apiVersion: airshipit.org/v1alpha1
 kind: Phase
@@ -31,7 +31,7 @@ config:
     apiVersion: airshipit.org/v1alpha1
     kind: KubernetesApply
     name: kubernetes-apply
-  documentEntryPoint: manifests/site/test-site/ephemeral/controlplane
+  documentEntryPoint: airshipctl/manifests/site/test-site/ephemeral/controlplane
 ---
 apiVersion: airshipit.org/v1alpha1
 kind: Phase
@@ -44,7 +44,7 @@ config:
     apiVersion: airshipit.org/v1alpha1
     kind: KubernetesApply
     name: kubernetes-apply
-  documentEntryPoint: manifests/site/test-site/target/initinfra
+  documentEntryPoint: airshipctl/manifests/site/test-site/target/initinfra
 ---
 apiVersion: airshipit.org/v1alpha1
 kind: Phase
@@ -57,7 +57,7 @@ config:
     apiVersion: airshipit.org/v1alpha1
     kind: KubernetesApply
     name: kubernetes-apply
-  documentEntryPoint: manifests/site/test-site/target/workers
+  documentEntryPoint: airshipctl/manifests/site/test-site/target/workers
 ---
 apiVersion: airshipit.org/v1alpha1
 kind: Phase
@@ -102,4 +102,4 @@ config:
     apiVersion: airshipit.org/v1alpha1
     kind: KubernetesApply
     name: kubernetes-apply
-  documentEntryPoint: manifests/site/test-site/target/workload
+  documentEntryPoint: airshipctl/manifests/site/test-site/target/workload
diff --git a/manifests/site/docker-test-site/shared/clusterctl/clusterctl.yaml b/manifests/site/docker-test-site/shared/clusterctl/clusterctl.yaml
index a3aa6c1ed..9ef33547c 100755
--- a/manifests/site/docker-test-site/shared/clusterctl/clusterctl.yaml
+++ b/manifests/site/docker-test-site/shared/clusterctl/clusterctl.yaml
@@ -16,16 +16,16 @@ providers:
   - name: "docker"
     type: "InfrastructureProvider"
     versions:
-      v0.3.7: manifests/function/capd/v0.3.7
+      v0.3.7: airshipctl/manifests/function/capd/v0.3.7
   - name: "kubeadm"
     type: "BootstrapProvider"
     versions:
-      v0.3.3: manifests/function/cabpk/v0.3.3
+      v0.3.3: airshipctl/manifests/function/cabpk/v0.3.3
   - name: "cluster-api"
     type: "CoreProvider"
     versions:
-      v0.3.3: manifests/function/capi/v0.3.3
+      v0.3.3: airshipctl/manifests/function/capi/v0.3.3
   - name: "kubeadm"
     type: "ControlPlaneProvider"
     versions:
-      v0.3.3: manifests/function/cacpk/v0.3.3
+      v0.3.3: airshipctl/manifests/function/cacpk/v0.3.3
diff --git a/pkg/config/repo.go b/pkg/config/repo.go
index 125503e6f..632301831 100644
--- a/pkg/config/repo.go
+++ b/pkg/config/repo.go
@@ -217,11 +217,10 @@ func (repo *Repository) ToAuth() (transport.AuthMethod, error) {
 // ToCheckoutOptions returns an instance of git.CheckoutOptions with
 // respective values(Branch/Tag/Hash) in checkout options initialized
 // CheckoutOptions describes how a checkout operation should be performed
-func (repo *Repository) ToCheckoutOptions(force bool) *git.CheckoutOptions {
-	co := &git.CheckoutOptions{
-		Force: force,
-	}
+func (repo *Repository) ToCheckoutOptions() *git.CheckoutOptions {
+	co := &git.CheckoutOptions{}
 	if repo.CheckoutOptions != nil {
+		co.Force = repo.CheckoutOptions.ForceCheckout
 		switch {
 		case repo.CheckoutOptions.Branch != "":
 			co.Branch = plumbing.NewBranchReferenceName(repo.CheckoutOptions.Branch)
@@ -238,19 +237,10 @@ func (repo *Repository) ToCheckoutOptions(force bool) *git.CheckoutOptions {
 // authentication and URL set
 // CloneOptions describes how a clone should be performed
 func (repo *Repository) ToCloneOptions(auth transport.AuthMethod) *git.CloneOptions {
-	cl := &git.CloneOptions{
+	return &git.CloneOptions{
 		Auth: auth,
 		URL:  repo.URLString,
 	}
-	if repo.CheckoutOptions != nil {
-		switch {
-		case repo.CheckoutOptions.Branch != "":
-			cl.ReferenceName = plumbing.NewBranchReferenceName(repo.CheckoutOptions.Branch)
-		case repo.CheckoutOptions.Tag != "":
-			cl.ReferenceName = plumbing.NewTagReferenceName(repo.CheckoutOptions.Tag)
-		}
-	}
-	return cl
 }
 
 // ToFetchOptions returns an instance of git.FetchOptions for given authentication
diff --git a/pkg/config/repo_test.go b/pkg/config/repo_test.go
index a82eaa0f2..7f7bbefd4 100644
--- a/pkg/config/repo_test.go
+++ b/pkg/config/repo_test.go
@@ -182,7 +182,7 @@ func TestToCheckout(t *testing.T) {
 	for _, name := range testCase.dataMapEntry {
 		repo := data.TestData[name]
 		require.NotNil(t, repo)
-		co := repo.ToCheckoutOptions(false)
+		co := repo.ToCheckoutOptions()
 		if testCase.expectedNil {
 			assert.Nil(t, co)
 		} else {
diff --git a/pkg/document/pull/pull.go b/pkg/document/pull/pull.go
index 5a1fe3369..72b9482f3 100644
--- a/pkg/document/pull/pull.go
+++ b/pkg/document/pull/pull.go
@@ -20,30 +20,20 @@ import (
 	"opendev.org/airship/airshipctl/pkg/log"
 )
 
-// Settings is a reference to environment.AirshipCTLSettings
-// AirshipCTLSettings is a container for all of the settings needed by airshipctl
-type Settings struct {
-	*config.Config
-}
-
 // Pull clones repositories
-func Pull(cfgFactory config.Factory) error {
+func Pull(cfgFactory config.Factory, noCheckout bool) error {
 	cfg, err := cfgFactory()
 	if err != nil {
 		return err
 	}
 
-	settings := &Settings{cfg}
-	if err = settings.cloneRepositories(); err != nil {
-		return err
-	}
-	return nil
+	return cloneRepositories(cfg, noCheckout)
 }
 
-func (s *Settings) cloneRepositories() error {
+func cloneRepositories(cfg *config.Config, noCheckout bool) error {
 	// Clone main repository
-	currentManifest, err := s.CurrentContextManifest()
-	log.Debugf("Reading current context manifest information from %s", s.LoadedConfigPath())
+	currentManifest, err := cfg.CurrentContextManifest()
+	log.Debugf("Reading current context manifest information from %s", cfg.LoadedConfigPath())
 	if err != nil {
 		return err
 	}
@@ -60,7 +50,7 @@ func (s *Settings) cloneRepositories() error {
 		}
 		log.Printf("Downloading %s repository %s from %s into %s",
 			repoName, repository.Name, extraRepoConfig.URL(), currentManifest.TargetPath)
-		err = repository.Download(extraRepoConfig.ToCheckoutOptions(true).Force)
+		err = repository.Download(noCheckout)
 		if err != nil {
 			return err
 		}
diff --git a/pkg/document/pull/pull_test.go b/pkg/document/pull/pull_test.go
index 44e84e1fa..e2a7dd580 100644
--- a/pkg/document/pull/pull_test.go
+++ b/pkg/document/pull/pull_test.go
@@ -81,14 +81,6 @@ func TestPull(t *testing.T) {
 			name:  "TestCloneRepositoriesMissingCheckoutOptions",
 			error: nil,
 		},
-		{
-			name: "TestCloneRepositoriesNonMasterBranch",
-			checkoutOpts: &config.RepoCheckout{
-				Branch:        "branch",
-				ForceCheckout: false,
-			},
-			error: nil,
-		},
 		{
 			name: "TestCloneRepositoriesInvalidOpts",
 			checkoutOpts: &config.RepoCheckout{
@@ -116,7 +108,7 @@ func TestPull(t *testing.T) {
 			currentManifest, err := cfg.CurrentContextManifest()
 			require.NoError(err)
 
-			err = pull.Pull(cfgFactory)
+			err = pull.Pull(cfgFactory, false)
 			if expectedErr != nil {
 				assert.NotNil(err)
 				assert.Equal(expectedErr, err)
diff --git a/pkg/document/repo/repo.go b/pkg/document/repo/repo.go
index 3664d386d..ef4a68a69 100644
--- a/pkg/document/repo/repo.go
+++ b/pkg/document/repo/repo.go
@@ -35,7 +35,7 @@ import (
 type OptionsBuilder interface {
 	ToAuth() (transport.AuthMethod, error)
 	ToCloneOptions(auth transport.AuthMethod) *git.CloneOptions
-	ToCheckoutOptions(force bool) *git.CheckoutOptions
+	ToCheckoutOptions() *git.CheckoutOptions
 	ToFetchOptions(auth transport.AuthMethod) *git.FetchOptions
 	URL() string
 }
@@ -79,7 +79,7 @@ func storerFromFs(fs billy.Filesystem) (storage.Storer, error) {
 }
 
 // Update fetches new refs, and checkout according to checkout options
-func (repo *Repository) Update(force bool) error {
+func (repo *Repository) Update() error {
 	log.Debugf("Updating repository %s", repo.Name)
 	if !repo.Driver.IsOpen() {
 		return ErrNoOpenRepo{}
@@ -92,15 +92,15 @@ func (repo *Repository) Update(force bool) error {
 	if err != nil && err != git.NoErrAlreadyUpToDate {
 		return fmt.Errorf("failed to fetch refs for repository %v: %w", repo.Name, err)
 	}
-	return repo.Checkout(force)
+	return repo.Checkout()
 }
 
 // Checkout git repository, ToCheckoutOptions method will be used go get CheckoutOptions
-func (repo *Repository) Checkout(enforce bool) error {
+func (repo *Repository) Checkout() error {
 	if !repo.Driver.IsOpen() {
 		return ErrNoOpenRepo{}
 	}
-	co := repo.ToCheckoutOptions(enforce)
+	co := repo.ToCheckoutOptions()
 	var branchHash string
 	if co.Hash == plumbing.ZeroHash {
 		branchHash = fmt.Sprintf("branch %s", co.Branch.String())
@@ -137,7 +137,7 @@ func (repo *Repository) Clone() error {
 // no remotes will be modified in this case, also no refs will be updated.
 // enforce parameter is used to simulate git reset --hard option.
 // If you want to enforce state of the repository, please delete current git repository before downloading.
-func (repo *Repository) Download(enforceCheckout bool) error {
+func (repo *Repository) Download(noCheckout bool) error {
 	log.Debugf("Attempting to download the repository %s", repo.Name)
 
 	if !repo.Driver.IsOpen() {
@@ -152,5 +152,8 @@ func (repo *Repository) Download(enforceCheckout bool) error {
 		}
 	}
 
-	return repo.Checkout(enforceCheckout)
+	if noCheckout {
+		return nil
+	}
+	return repo.Checkout()
 }
diff --git a/pkg/document/repo/repo_test.go b/pkg/document/repo/repo_test.go
index 4a8158216..815cc87bd 100644
--- a/pkg/document/repo/repo_test.go
+++ b/pkg/document/repo/repo_test.go
@@ -44,7 +44,7 @@ func (md mockBuilder) ToAuth() (transport.AuthMethod, error) {
 func (md mockBuilder) ToCloneOptions(transport.AuthMethod) *git.CloneOptions {
 	return md.CloneOptions
 }
-func (md mockBuilder) ToCheckoutOptions(bool) *git.CheckoutOptions {
+func (md mockBuilder) ToCheckoutOptions() *git.CheckoutOptions {
 	return md.CheckoutOptions
 }
 func (md mockBuilder) ToFetchOptions(transport.AuthMethod) *git.FetchOptions {
@@ -131,15 +131,15 @@ func TestUpdate(t *testing.T) {
 	require.NotEqual(t, prevCommitHash.String(), headHash.String())
 	builder.CheckoutOptions = &git.CheckoutOptions{Hash: *prevCommitHash}
 	// Checkout previous commit
-	err = repo.Checkout(true)
+	err = repo.Checkout()
 	require.NoError(t, err)
 
 	// Set checkout back to master
 	builder.CheckoutOptions = checkout
-	err = repo.Checkout(true)
+	err = repo.Checkout()
 	assert.NoError(t, err)
 	// update repository
-	require.NoError(t, repo.Update(true))
+	require.NoError(t, repo.Update())
 
 	currentHash, err := repo.Driver.Head()
 	assert.NoError(t, err)
@@ -147,7 +147,7 @@ func TestUpdate(t *testing.T) {
 	assert.Equal(t, headHash.String(), currentHash.Hash().String())
 
 	repo.Driver.Close()
-	updateError := repo.Update(true)
+	updateError := repo.Update()
 	assert.Error(t, updateError)
 }
 
@@ -206,6 +206,6 @@ func TestCheckout(t *testing.T) {
 
 	repo, err := NewRepository(".", builder)
 	require.NoError(t, err)
-	err = repo.Checkout(true)
+	err = repo.Checkout()
 	assert.Error(t, err)
 }
diff --git a/roles/airshipctl-run-script/tasks/main.yaml b/roles/airshipctl-run-script/tasks/main.yaml
index 70fe843da..fb9a09688 100644
--- a/roles/airshipctl-run-script/tasks/main.yaml
+++ b/roles/airshipctl-run-script/tasks/main.yaml
@@ -19,6 +19,5 @@
   vars:
     default_zuul_dir: "{{ ansible_user_dir }}/{{ zuul.project.src_dir }}"
   environment:
-    AIRSHIP_CONFIG_MANIFEST_DIRECTORY: "{{ remote_work_dir | default(local_src_dir) | default(default_zuul_dir) }}"
-    AIRSHIP_SITE_NAME: "manifests/site/{{ site | default('test-site') }}"
+    AIRSHIP_CONFIG_PRIMARY_REPO_URL: "{{ remote_work_dir | default(local_src_dir) | default(default_zuul_dir) }}"
     SITE_NAME: "{{ site | default('test-site') }}"
diff --git a/tools/deployment/22_test_configs.sh b/tools/deployment/22_test_configs.sh
index f64c1f01e..0f165784c 100755
--- a/tools/deployment/22_test_configs.sh
+++ b/tools/deployment/22_test_configs.sh
@@ -34,8 +34,8 @@ export SYSTEM_ACTION_RETRIES=30
 export SYSTEM_REBOOT_DELAY=30
 export AIRSHIP_CONFIG_PRIMARY_REPO_BRANCH=${BRANCH:-"master"}
 # the git repo url or local file system path to a cloned repo, e.g., /home/stack/airshipctl
-export AIRSHIP_CONFIG_PRIMARY_REPO_URL=${REPO:-"https://review.opendev.org/airship/airshipctl"}
-export AIRSHIP_SITE_NAME=${AIRSHIP_SITE_NAME:-"manifests/site/test-site"}
+export AIRSHIP_CONFIG_PRIMARY_REPO_URL=${AIRSHIP_CONFIG_PRIMARY_REPO_URL:-"https://review.opendev.org/airship/airshipctl"}
+export AIRSHIP_CONFIG_PRIMARY_REPO_NAME=${AIRSHIP_CONFIG_PRIMARY_REPO_NAME:-"airshipctl"}
 export AIRSHIP_CONFIG_MANIFEST_DIRECTORY=${AIRSHIP_CONFIG_MANIFEST_DIRECTORY:-"/tmp/airship"}
 export EPHEMERAL_CONFIG_CA_DATA=$(cat tools/deployment/certificates/ephemeral_config_ca_data| base64 -w0)
 export EPHEMERAL_IP=${EPHEMERAL_IP:-"10.23.25.101"}
diff --git a/tools/deployment/23_pull_documents.sh b/tools/deployment/23_pull_documents.sh
index 608d7fbaf..830d19ad1 100755
--- a/tools/deployment/23_pull_documents.sh
+++ b/tools/deployment/23_pull_documents.sh
@@ -15,4 +15,4 @@
 set -xe
 
 echo "Pull site documents using airshipctl"
-airshipctl document pull --debug
+airshipctl document pull -n --debug
diff --git a/tools/deployment/templates/airshipconfig_template b/tools/deployment/templates/airshipconfig_template
index 977a4dabe..24112dd1d 100644
--- a/tools/deployment/templates/airshipconfig_template
+++ b/tools/deployment/templates/airshipconfig_template
@@ -28,6 +28,5 @@ manifests:
           remoteRef: ""
           tag: ""
         url: ${AIRSHIP_CONFIG_PRIMARY_REPO_URL}
-    metadataPath: manifests/metadata.yaml
-    subPath: ${AIRSHIP_SITE_NAME}
+    metadataPath: airshipctl/manifests/metadata.yaml
     targetPath: ${AIRSHIP_CONFIG_MANIFEST_DIRECTORY}
diff --git a/tools/document/validate_site_docs.sh b/tools/document/validate_site_docs.sh
index 5c2c73497..91d003ffe 100755
--- a/tools/document/validate_site_docs.sh
+++ b/tools/document/validate_site_docs.sh
@@ -16,11 +16,10 @@ set -xe
 
 # The root of the manifest structure to be validated.
 # This corresponds to the targetPath in an airshipctl config
-: ${MANIFEST_ROOT:="${PWD}"}
+: ${MANIFEST_ROOT:="$(dirname "${PWD}")"}
 # The location of sites whose manifests should be validated.
-# This are relative to MANIFEST_ROOT above, and correspond to
-# the base of the subPath in an airshipctl config
-: ${SITE_ROOT:="manifests/site"}
+# This are relative to MANIFEST_ROOT above
+: ${SITE_ROOT:="$(basename "${PWD}")/manifests/site"}
 
 : ${SITE:="test-workload"}
 : ${CONTEXT:="kind-airship"}
@@ -78,7 +77,6 @@ manifests:
           force: false
           tag: ""
         url: https://opendev.org/airship/treasuremap
-    subPath: ${SITE_ROOT}/${SITE}
     targetPath: ${MANIFEST_ROOT}
 EOL
 }
@@ -103,8 +101,6 @@ for cluster in ephemeral target; do
         sed -i "s/${CONTEXT}/${CONTEXT}_${cluster}/" ${AIRSHIPKUBECONFIG}
         generate_airshipconf ${cluster}
 
-        ${ACTL} cluster init
-
         # A sequential list of potential phases.  A fancier attempt at this has been
         # removed since it was choking in certain cases and got to be more trouble than was worth.
         # This should be removed once we have a phase map that is smarter.
diff --git a/tools/gate/20_run_gate_runner.sh b/tools/gate/20_run_gate_runner.sh
index 8522426df..b9f372ac8 100755
--- a/tools/gate/20_run_gate_runner.sh
+++ b/tools/gate/20_run_gate_runner.sh
@@ -23,6 +23,7 @@ TMP_DIR=${TMP_DIR:-"$(dirname $(mktemp -u))"}
 ANSIBLE_HOSTS=${ANSIBLE_HOSTS:-"${TMP_DIR}/ansible_hosts"}
 PLAYBOOK_CONFIG=${PLAYBOOK_CONFIG:-"${TMP_DIR}/config.yaml"}
 export AIRSHIPCTL_WS=${AIRSHIPCTL_WS:-$PWD}
+export AIRSHIP_CONFIG_PRIMARY_REPO_URL=${AIRSHIP_CONFIG_PRIMARY_REPO_URL:-$PWD}
 
 sudo --preserve-env=AIRSHIPCTL_WS ansible-playbook -i "$ANSIBLE_HOSTS" \
 	playbooks/airshipctl-gate-runner.yaml \
diff --git a/tools/validate_docs b/tools/validate_docs
index 4edbfc505..dbe2b05aa 100755
--- a/tools/validate_docs
+++ b/tools/validate_docs
@@ -18,11 +18,10 @@ set -xe
 
 # The root of the manifest structure to be validated.
 # This corresponds to the targetPath in an airshipctl config
-: ${MANIFEST_ROOT:="${PWD}"}
+: ${MANIFEST_ROOT:="$(dirname "${PWD}")"}
 # The space-separated locations of sites whose manifests should be validated.
-# These are relative to MANIFEST_ROOT above, and correspond to
-# the base of the subPath in an airshipctl config
-: ${SITE_ROOTS:="manifests/site"}
+# These are relative to MANIFEST_ROOT above
+: ${SITE_ROOTS:="$(basename "${PWD}")/manifests/site"}
 
 # get kind
 echo "Fetching kind from ${KIND_URL}..."
diff --git a/zuul.d/jobs.yaml b/zuul.d/jobs.yaml
index b7f8e92d2..74044b871 100644
--- a/zuul.d/jobs.yaml
+++ b/zuul.d/jobs.yaml
@@ -91,6 +91,7 @@
         - ./tools/deployment/02_install_clusterctl.sh
         # 21_systemwide_executable.sh is run in the build-gate pre-run above
         - ./tools/deployment/22_test_configs.sh
+        - ./tools/deployment/23_pull_documents.sh
         - ./tools/deployment/24_build_ephemeral_iso.sh
         - ./tools/deployment/25_deploy_ephemeral_node.sh
         - ./tools/deployment/26_deploy_metal3_capi_ephemeral_node.sh