Ive made a few changes the the apktool for android. First off it will be installed to they system partition. The apktool data folder will also be in system partition, so don't forget to set it when you start the app. Reason being is the emulated SD doesn't allow executing of files. If you want to use the app to unpack/repack and tweak your boot.img. Make a working directory in the apktool folder and place the boot.img in it then unpack and tweak. You have to options so choose the "common" unpack and repack when it asks.
I wanted to make this a universal system install. So before you flash just mount your system partition because the script will not. Won't hurt nothing it just simply won't install unless system is mounted.
It will work on whatever ROM you're using to save any questions.
here's the link flash it and modify some apps right on your phone. Its fully tested and it works great
Sent from my One Mini
CLICK ON ANDROID TO ACCESS MY WORKING FOLDER