Yesterday (3/10/14) when iOS 7.1 was released I also upgraded to Xcode 5.1 and found that my PhoneGap/Cordova project would no longer compile to my iPhone 5s. I also upgrade
You just have to add the arm64 architecture on every statement and building setting, i mean, on your current project, and on the cordova project.
On your project:
on Cordova:
AND THE MOST IMPORTANT
-Valid architectures at cordova build settings
This configuration generates a lot of warnings, but is just change the "%d" for "%ld" at all lines that the warning says.