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/welcome/appmanager.go b/core/installer/welcome/appmanager.go
index 8a4bf34..39d5c3c 100644
--- a/core/installer/welcome/appmanager.go
+++ b/core/installer/welcome/appmanager.go
@@ -91,7 +91,7 @@
 	if err != nil {
 		return err
 	}
-	instances, err := s.m.FindAllInstances(slug)
+	instances, err := s.m.FindAllAppInstances(slug)
 	if err != nil {
 		return err
 	}
@@ -269,7 +269,7 @@
 	if err != nil {
 		return err
 	}
-	instances, err := s.m.FindAllInstances(slug)
+	instances, err := s.m.FindAllAppInstances(slug)
 	if err != nil {
 		return err
 	}
@@ -304,7 +304,7 @@
 	if err != nil {
 		return err
 	}
-	instances, err := s.m.FindAllInstances(a.Name())
+	instances, err := s.m.FindAllAppInstances(a.Name())
 	if err != nil {
 		return err
 	}
diff --git a/core/installer/welcome/welcome.go b/core/installer/welcome/welcome.go
index a820586..fe6c560 100644
--- a/core/installer/welcome/welcome.go
+++ b/core/installer/welcome/welcome.go
@@ -205,7 +205,7 @@
 		return
 	}
 	{
-		appManager, err := installer.NewAppManager(s.repo, s.nsCreator)
+		appManager, err := installer.NewAppManager(s.repo, s.nsCreator, "/apps")
 		if err != nil {
 			http.Error(w, err.Error(), http.StatusInternalServerError)
 			return
@@ -250,7 +250,7 @@
 }
 
 func (s *Server) initMemberships(username string) error {
-	return s.repo.Atomic(func(r installer.RepoFS) (string, error) {
+	return s.repo.Do(func(r installer.RepoFS) (string, error) {
 		var fa firstaccount
 		if err := installer.ReadYaml(r, "first-account.yaml", &fa); err != nil {
 			return "", err