diff --git a/cmd/plural/up.go b/cmd/plural/up.go
index cbdc2223..ece81ba4 100644
--- a/cmd/plural/up.go
+++ b/cmd/plural/up.go
@@ -32,8 +32,6 @@ func (p *Plural) handleUp(c *cli.Context) error {
 		return err
 	}
 
-	defer ctx.Cleanup()
-
 	if err := ctx.Backfill(); err != nil {
 		return err
 	}
diff --git a/pkg/up/deploy.go b/pkg/up/deploy.go
index 3b50eced..012fb7c4 100644
--- a/pkg/up/deploy.go
+++ b/pkg/up/deploy.go
@@ -23,13 +23,13 @@ func (ctx *Context) Deploy(commit func() error) error {
 	}
 
 	if err := runAll([]terraformCmd{
-		{dir: "./clusters", cmd: "init", args: []string{"-upgrade"}},
-		{dir: "./clusters", cmd: "apply", args: []string{"-auto-approve"}, retries: 1},
+		{dir: "./terraform/mgmt", cmd: "init", args: []string{"-upgrade"}},
+		{dir: "./terraform/mgmt", cmd: "apply", args: []string{"-auto-approve"}, retries: 1},
 	}); err != nil {
 		return err
 	}
 
-	stateCmd := &terraformCmd{dir: "./clusters"}
+	stateCmd := &terraformCmd{dir: "./terraform/mgmt"}
 	outs, err := stateCmd.outputs()
 	if err != nil {
 		return err
@@ -56,16 +56,20 @@ func (ctx *Context) Deploy(commit func() error) error {
 
 	utils.Highlight("\nSetting up gitops management...\n")
 
-	return runAll([]terraformCmd{
-		{dir: "./apps/terraform", cmd: "init", args: []string{"-upgrade"}},
-		{dir: "./apps/terraform", cmd: "apply", args: []string{"-auto-approve"}, retries: 1},
-	})
+	if err := runAll([]terraformCmd{
+		{dir: "./terraform/apps", cmd: "init", args: []string{"-upgrade"}},
+		{dir: "./terraform/apps", cmd: "apply", args: []string{"-auto-approve"}, retries: 1},
+	}); err != nil {
+		return err
+	}
+
+	return ctx.Prune()
 }
 
 func (ctx *Context) Destroy() error {
 	return runAll([]terraformCmd{
-		{dir: "./clusters", cmd: "init", args: []string{"-upgrade"}},
-		{dir: "./clusters", cmd: "destroy", args: []string{"-auto-approve"}, retries: 2},
+		{dir: "./terraform/mgmt", cmd: "init", args: []string{"-upgrade"}},
+		{dir: "./terraform/mgmt", cmd: "destroy", args: []string{"-auto-approve"}, retries: 2},
 	})
 }
 
diff --git a/pkg/up/generate.go b/pkg/up/generate.go
index 275163f4..5c46b35d 100644
--- a/pkg/up/generate.go
+++ b/pkg/up/generate.go
@@ -21,7 +21,7 @@ func (ctx *Context) Cleanup() {
 
 func (ctx *Context) Generate() error {
 	if !utils.Exists("./bootstrap") {
-		if err := git.BranchedSubmodule("https://github.com/pluralsh/bootstrap.git", "stacks-support"); err != nil {
+		if err := git.BranchedSubmodule("https://github.com/pluralsh/bootstrap.git", "refactored-up"); err != nil {
 			return err
 		}
 	}
@@ -31,11 +31,11 @@ func (ctx *Context) Generate() error {
 		{from: "./bootstrap/charts/runtime/values.yaml.tpl", to: "./helm-values/runtime.yaml", overwrite: true},
 		{from: "./bootstrap/helm/certmanager.yaml", to: "./helm-values/certmanager.yaml", overwrite: true},
 		{from: "./bootstrap/helm/flux.yaml", to: "./helm-values/flux.yaml", overwrite: true},
-		{from: fmt.Sprintf("./bootstrap/templates/providers/bootstrap/%s.tf", prov), to: "clusters/provider.tf"},
-		{from: fmt.Sprintf("./bootstrap/templates/setup/providers/%s.tf", prov), to: "clusters/mgmt.tf"},
-		{from: "./bootstrap/templates/setup/console.tf", to: "clusters/console.tf"},
-		{from: fmt.Sprintf("./bootstrap/templates/providers/apps/%s.tf", prov), to: "apps/terraform/provider.tf"},
-		{from: "./bootstrap/templates/setup/cd.tf", to: "apps/terraform/cd.tf"},
+		{from: fmt.Sprintf("./bootstrap/templates/providers/bootstrap/%s.tf", prov), to: "terraform/mgmt/provider.tf"},
+		{from: fmt.Sprintf("./bootstrap/templates/setup/providers/%s.tf", prov), to: "terraform/mgmt/mgmt.tf"},
+		{from: "./bootstrap/templates/setup/console.tf", to: "terraform/mgmt/console.tf"},
+		{from: fmt.Sprintf("./bootstrap/templates/providers/apps/%s.tf", prov), to: "terraform/apps/provider.tf"},
+		{from: "./bootstrap/templates/setup/cd.tf", to: "terraform/apps/cd.tf"},
 		{from: "./bootstrap/README.md", to: "README.md", overwrite: true},
 	}
 
@@ -52,7 +52,7 @@ func (ctx *Context) Generate() error {
 
 	copies := []templatePair{
 		{from: "./bootstrap/terraform/modules/clusters", to: "terraform/modules/clusters"},
-		{from: fmt.Sprintf("./bootstrap/terraform/clouds/%s", prov), to: "terraform/modules/mgmt"},
+		{from: fmt.Sprintf("./bootstrap/terraform/clouds/%s", prov), to: "terraform/mgmt/cluster"},
 		{from: "./bootstrap/apps/repositories", to: "apps/repositories"},
 		{from: "./bootstrap/apps/services", to: "apps/services"},
 		{from: "./bootstrap/templates", to: "templates"},
diff --git a/pkg/up/prune.go b/pkg/up/prune.go
new file mode 100644
index 00000000..1b2e873a
--- /dev/null
+++ b/pkg/up/prune.go
@@ -0,0 +1,48 @@
+package up
+
+import (
+	"os"
+	"os/exec"
+
+	"github.com/pluralsh/plural-cli/pkg/utils"
+	"github.com/pluralsh/plural-cli/pkg/utils/git"
+)
+
+func (ctx *Context) Prune() error {
+	utils.Highlight("\nCleaning up unneeded resources...\n\n")
+	repoRoot, err := git.Root()
+	if err != nil {
+		return err
+	}
+
+	toRemove := []string{
+		"null_resource.console",
+		"helm_release.certmanager",
+		"helm_release.flux",
+		"helm_release.runtime",
+		"helm_release.console",
+	}
+
+	for _, field := range toRemove {
+		if err := stateRm("./terraform/mgmt", field); err != nil {
+			return err
+		}
+	}
+
+	if err := os.Remove("./terraform/mgmt/console.tf"); err != nil {
+		return err
+	}
+
+	_ = os.RemoveAll("./terraform/apps")
+	ctx.Cleanup()
+
+	return git.Sync(repoRoot, "Post-setup resource cleanup", true)
+}
+
+func stateRm(dir, field string) error {
+	cmd := exec.Command("terraform", "state", "rm", field)
+	cmd.Dir = dir
+	cmd.Stdout = os.Stdout
+	cmd.Stderr = os.Stderr
+	return cmd.Run()
+}