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/activate.go b/core/installer/tasks/activate.go
index dffdfbe..ccbdbb8 100644
--- a/core/installer/tasks/activate.go
+++ b/core/installer/tasks/activate.go
@@ -31,7 +31,7 @@
 			return err
 		}
 		repoHost := strings.Split(st.ssClient.Addr, ":")[0]
-		return st.repo.Atomic(func(r installer.RepoFS) (string, error) {
+		return st.repo.Do(func(r installer.RepoFS) (string, error) {
 			kust, err := installer.ReadKustomization(r, "environments/kustomization.yaml")
 			if err != nil {
 				return "", err