After submitting a 8u40 app with the corrected Yosemite signing code (RT-40016) the Applicaiton Loader for the Mac App Store responds with the following error:

ERROR ITMS-90239: "Invalid Signature. Code object is not signed at all. The binary at path [Smoke Test.app/Contents/MacOS/Smoke Test] contains an invalid signature. Make sure you have signed your application with a distribution certificate, not an ad hoc certificate or a development certificate. Verify that the code signing settings in Xcode are correct at the target level (which override any values at the project level). If you are certain your code signing settings are correct, choose "Clean All" in Xcode, delete the "build" directory in the Finder, and rebuild your release target. For more information, please consult https://developer.apple.com/library/mac/documentation/Security/Conceptual/CodeSigningGuide/Introduction/Introduction.html"

Note that the application validates locally with codesign --verify and codesign --verify --deep (which it didn't before RT-40016).