But I think you still need to remove some files or use our Runtime Shrinker.
The OLEWrapper file must be removed as it can't be code signed.
And Sam can improve his app to do that, too.
I did a couple of tests with him and as far as I can see no additional steps are needed anymore - everything is done by Appwrapper and the codesigned app stays stable with upload, downloading, zipping and unzipping. For more technical details you might contact Sam from Ohanaware directly.
Sadly enough, longer tests showed, that it didn´t work.
We solved the problem and you can read on my blog how to sign a runtime now for Mavericks and upcoming Yosemite:
Many Thanks, Christian!
Wow! Great work! I've been hoping Yosemite might be the solution but looks like it takes a monkey as well! This has been a thorn in our side for too long. Thanks for finding a way through the thicket.