Rewrite: rewrites env config repo and commits application cue files

We can build upon this tool to implement version to version migration logic.

Change-Id: I6066f565f118ca44ca3ce7a0ac7522258958cf25
diff --git a/core/installer/tasks/infra.go b/core/installer/tasks/infra.go
index fb3047d..543cc67 100644
--- a/core/installer/tasks/infra.go
+++ b/core/installer/tasks/infra.go
@@ -23,7 +23,7 @@
 		if err != nil {
 			return err
 		}
-		appManager, err := installer.NewAppManager(r, st.nsCreator)
+		appManager, err := installer.NewAppManager(r, st.nsCreator, "/apps")
 		if err != nil {
 			return err
 		}
@@ -61,7 +61,7 @@
 		if err != nil {
 			return err
 		}
-		r.Atomic(func(r installer.RepoFS) (string, error) {
+		r.Do(func(r installer.RepoFS) (string, error) {
 			{
 				// TODO(giolekva): private domain can be configurable as well
 				config := installer.AppEnvConfig{
@@ -127,7 +127,7 @@
 		if err != nil {
 			return err
 		}
-		return r.Atomic(func(r installer.RepoFS) (string, error) {
+		return r.Do(func(r installer.RepoFS) (string, error) {
 			fa := firstAccount{false, initGroups}
 			if err := installer.WriteYaml(r, "first-account.yaml", fa); err != nil {
 				return "", err