I have an account with Codiqa, and I've created my mobile reference app. It provides a utility to export your .zip package compiled for PhoneGap by adobe. When I import it, it works fine as a drag/drop app via USB cable. But to sell it on the app store, I have to generate a license key. That would be no problem if I compiled it via Eclipse, but since I didn't, I think there is no way to generate a key for it.it seems Codiqa doesn't provide support for that and I have the rest of the process set up.
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Sorry to hear that you're having trouble, I'm an intern at Drifty, the company that makes Codiqa.
When you select export in Codiqa, what you receive is a source code bundle for Eclipse (if you're using Android, or Xcode for iOS). Then you can load the source package into Eclipse using project import and do the signing and generate the apk the way you would any other PhoneGap or Android project.
You said you didn't compile using Eclipse, but using Ant or PhoneGap Build will be similar to building with Eclipse.
Hope that helps! :)

user1234
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1Thank you! So I should import to Eclipse, compile there, and get the .apk from that? Tell your supervisor that you're my savior. :) – Jay Noe Jul 12 '13 at 22:53
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Okay, but now Codiqa automatically applies the package to be com.codiqa.project. I've tried editing it and changing all the variables, and now it just says that the app has stopped in the debugger. – Jay Noe Jul 13 '13 at 01:11
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2Yep, import to Eclipse and then compile. You can change the package name before you run the application, make sure you also change the folder structure where the .java file is. – Max Jul 17 '13 at 23:19