After upgrading to Xcode 6.3.1, I got a new error that I haven’t received before:
ERROR ITMS-90035: "Invalid Signature. Code object is not signed at all..."
The error popped up every time I tried to submit apps to the App Store, even old apps that were perfectly submittable before upgrading Xcode to 6.3.1.
Turns out that the problem was caused by an .sh file in one of the external libs used by the app. Previously, archiving apps with this .sh file worked great, but not anymore.
Since this .sh file was not needed by the app, I just removed the file reference and kept the file on disk. If you run into the same error code, I hope this will solve your problem.