Android deployment bails out with exit code 12

I've compiled Qt 5.3.0 alpha myself on Kubuntu 14.04 32 bit (more info below).

When I try to deploy any project (even a clean template from Qt Creator) to an Android device (I've tried both the Simulator and a real device: Samsung Galaxy S2; I've tried both with API 16 and API 19), androiddeployqt fails with error code 12.

When running in verbose mode, I can see what is missing:
Cannot find /projectPath/android-build/res/values/libs.xml in prepared packaged. This file is required.

Apart from the fact that the message has an error ("prepared packaged"... he?), it causes the whole deployment to be aborted.

I have tried running the same project using Qt 5.2.1, and it works without a problem. I've also tried deploying with 5.3.0 alpha, but using androiddeployqt from 5.2.1: still the same error. I've tried all this with various Qt Creators, too: 3.0.0, 3.0.1, 3.1.0 beta (newest snapshot from qt-project.org).

I have also tried compiling Qt 5.3.0 from git (both stable and dev branches): still does not work.

This is the configure line I have used:
../qt-src/configure -xplatform android-g++ -nomake tests -nomake examples -android-ndk /path/to/ndk -android-sdk /path/to/sdk -android-ndk-host linux-x86 -android-toolchain-version 4.8 -skip qttranslations -skip qtwebkit -skip qtserialport -skip qtwebkit-examples -no-warnings-are-errors -skip qtquick1 -opensource -confirm-license -prefix $PWD/qtbase

If there is any information missing, please tell me.

EDIT I have some new data. I have completely recompiled the alpha package, but this time, instead of doing an out-of-source, prefixed build, I have just cded into Qt source directory, and run ./configure +all flags, and -developer-build instead of -prefix. Now it works!

So it seems that Qt for Android does not expect a prefixed, out-of-source build. In my opinion, this is a bug, but probably very minor, as not many people compile Qt in the same way I do