AppRunner: Create .git directory when cloning repository

Change-Id: I733fd2aad5d7ec67c38cb773097b12b86ed69755
diff --git a/apps/app-runner/server.go b/apps/app-runner/server.go
index 89f621a..e917754 100644
--- a/apps/app-runner/server.go
+++ b/apps/app-runner/server.go
@@ -151,7 +151,7 @@
 			Commands: []CommandStatus{},
 		}
 	}
-	if s.agentMode {
+	if s.agentMode && s.repoAddr == "" {
 		if _, err := os.Stat(filepath.Join(newDir, ".git")); err != nil && os.IsNotExist(err) {
 			commands = append(commands, command{cmd: "git config --global user.name dodo"})
 			s.status.Commands = append(s.status.Commands, CommandStatus{