Hello,
The first thing I noticed after testing the exporter is that our plugin prelude is missing in the exportation (I will try to solve it later). So if you were trying to use the plugin, it won't work.
Apart from that, after exporting, are you just compressing the folder and uploading it to the cloud? If so, that might be the problem. The cloud compiler is expecting a www folder + a config.xml file.
I need to have a further look at this issue, but I hope this can help a little.
In addition:
Does anyone know if there is any way to debug this error deeper than using the "default" cocoonJS launcher console?
You can try the "adb logcat" command for Android or the device log provided by xcode.
Oh, and one thing more: the cordova.js file is something that cordova will add automatically to your project. Do not worry for that.
Regards.