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/init.go b/core/installer/tasks/init.go
index 70b7939..4e676cd 100644
--- a/core/installer/tasks/init.go
+++ b/core/installer/tasks/init.go
@@ -104,7 +104,7 @@
 		if err != nil {
 			return err
 		}
-		if err := repoIO.Atomic(func(r installer.RepoFS) (string, error) {
+		if err := repoIO.Do(func(r installer.RepoFS) (string, error) {
 			w, err := r.Writer("README.md")
 			if err != nil {
 				return "", err