Extract the Android .odex files and package a new android.jar with the retrieved classes

packageAndroid.sh

#!/bin/sh
##
# Usage:
# ./convert.sh /path/to/framework /path/to/out $apiVersion $arch
# 
# $arch is mandatory only in case of an ART system and defines the boot folder to use (arm, x86, x86_64).
##
frameworkDir=$1

# Final output directory
if [ -z $2 ];
then
    outDir=out
else
    outDir=$2
fi
[[ -d $outDir ]] || mkdir -p $outDir

# Target API Version, 
# useful to detect Dalvik/ART platforms
if [ -z $3 ];
then
    apiVersion=15
else
    apiVersion=$3
fi

# Target architecture,
# which is needed for ART build
if [ -z $4 ];
then
    arch="x86"
else
    arch=$4
fi;


##
# Convert *.odex file to smali code, 
# then build *.dex file back from it.
#
# The baksmali method we are using will limit us to API 23+ for ART systems
# and 20- for Dalvik systems
#
# There is a no-go zone for API 21 and 22 
# See: https://github.com/JesusFreke/smali/issues/392   
##
function odex2dex {
    # Inputs
    odexDir=$1
    outputDir=$2
    
    ## Workspace dependencies
    smali="smali.jar"
    baksmali="baksmali.jar"
    [[ -f $smali ]] || curl -L https://bitbucket.org/JesusFreke/smali/downloads/smali-2.2.0.jar -o $smali
    [[ -f $baksmali ]] || curl -L https://bitbucket.org/JesusFreke/smali/downloads/baksmali-2.2.0.jar -o $baksmali

    if [ $apiVersion -ge 21 ]; then
        baksmaliCP="boot.oat"
        frameworkWorkDir="$frameworkDir/$arch"
    else
        baksmaliCP=":core.jar:bouncycastle.jar:ext.jar:framework.jar:android.policy.jar:services.jar:core-junit.jar"
        frameworkWorkDir=$frameworkDir
    fi

    # Actual process 
    [[ -d $frameworkWorkDir ]] || $(echo "Boot classpath directory $frameworkWorkDir not found!" && exit 1)
    for file in $(ls $odexDir/*.odex)
    do
        fileName=$(basename $file)
        libName=${fileName%.*} # Remove the trailing extension
        libSmali="$outputDir/$libName-smali"
        dexFile="$outputDir/$libName.dex"

        echo "Transforming odex lib: $libName (smali: $libSmali - dex: $dexFile)"
        echo "[DEBUG] cp: $baksmaliCP"

        # Exctract odex files
        java -jar $baksmali deodex -a $apiVersion -c $baksmaliCP -d $frameworkWorkDir -o $libSmali $file
        # Convert the smali files to simple dex files
        java -jar $smali assemble -a $apiVersion -o $dexFile $libSmali
    done;
}

##
# Takes decompressed .dex files from $1 
# and assemble corresponding .class jar files in $2.
##
function dex2jar {
    # Inputs
    dexDir=$1
    outputDir=$2
    
    ## Workspace dependencies
    d2jZip="d2j-2.0.zip"
    d2jDir="dex2jar"
    d2jBin="$d2jDir/dex2jar-2.0"
    d2j="$d2jBin/d2j-dex2jar.sh"
    chmod +x $d2jBin/*.sh
    [[ -f $d2j ]] || $(curl -L https://github.com/pxb1988/dex2jar/releases/download/2.0/dex-tools-2.0.zip -o $d2jZip \
        && unzip $d2jZip -d $d2jDir)
    rm $d2jZip

    for file in $(ls $dexDir/*.dex);
    do
        fileName=$(basename $file)
        libName=${fileName%.*} # Remove the trailing extension
        jarFile=$outputDir/$libName.jar

        echo "Converting dex $file to jar: $jarFile"
        ./$d2j --force -o $jarFile $file
    done
}

##
# Unzip every .jar file from the $1 dir
# and creates a single jar file in the $2 dir.
##
function bundleAndroidJar {
    jarInput=$1
    outputDir=$2
    jarContent="$outputDir/unzippedJars"
    [[ -d $jarContent ]] || mkdir $jarContent

    for file in $(ls $jarInput/*.jar)
    do
        echo "Adding $file to final jar"
        unzip -o $file -d $jarContent
    done;
    output=android-$apiVersion-custom.jar
    cd $jarContent && jar cf $output * && cd -
    mv $jarContent/$output $outputDir
}


## Defining common work directories
# Contains the extracted dex files for each previous jar
tmpDex="$outDir/dex2jar-output"
[[ -d $tmpDex ]] || mkdir $tmpDex
# Contains every final framework jars
jarDir="$outDir/jars"
[[ -d $jarDir ]] || mkdir $jarDir
 
if [ $apiVersion -ge 21 ];
then
    ## If using ART instead of Dalvik, the framework directory should look like:
    # framework     -- *.jar (stubs)
    # ├── oat       -- API 23+ (!)
    # │   └── $arch -- *.odex
    # └── $arch     -- boot*.{oat,art} (framework implementation)
    ##
    echo "Disassembling post Lollipop version, using oat2dex tool"

    # Currently using v2.2b4
    oat2Dex="oat2Dex.jar"
    [[ -f $oat2Dex ]] || curl -L https://github.com/testwhat/SmaliEx/releases/download/snapshot-s/oat2dex.jar -o $oat2Dex
    
    # Contains the raw results of oat2dex
    tmpO2D="$outDir/oat2dex-output" 
    [[ -d $tmpO2D ]] || mkdir $tmpO2D

    ## There seems to be a bug with oat2Dex no copying all jars
    bootJar="$tmpO2D/boot-jar-original"
    [[ -d $bootJar ]] || mkdir $bootJar
    cp $frameworkDir/*.jar $bootJar
    #

    java -jar $oat2Dex -o $tmpO2D devfw $frameworkDir 
    cp $tmpO2D/framework-odex/*.odex $tmpDex
    cp $tmpO2D/framework-jar-original/*.jar $tmpDex
    cp $tmpO2D/odex/*.dex $tmpDex
    cp $tmpO2D/boot-jar-original/*.jar $tmpDex
else
    ## If using Dalvik, the framework directory should look like:
    # framework  -- *.{jar,odex}
    ## 
    echo "Disassembling Dalvik image, using baksmali"

    # This script is assuming that every
    # *.jar, and *.odex files are in the same folder.
    ## TODO: `find | cp` ?
    cp $frameworkDir/{*.odex,*.jar} $tmpDex
fi;

echo "Transforming framework to a single jar (api: $apiVersion, framework: $frameworkDir)"
odex2jar $tmpDex $jarDir
dex2jar $tmpDex $jarDir
bundleAndroidJar $jarDir $outDir

Updated Links (cURL/wGet compatible):

May 5th 2020: originals
https://repo1.maven.org/maven2/org/smali/smali/2.4.0/smali-2.4.0.jar
https://repo1.maven.org/maven2/org/smali/baksmali/2.4.0/baksmali-2.4.0.jar
https://repo1.maven.org/maven2/org/smali/dexlib2/2.4.0/dexlib2-2.4.0.jar
https://repo1.maven.org/maven2/org/smali/util/2.4.0/util-2.4.0.jar

or

June 4th 2018: oat2dex (v0.90) with modified smali/baksmali (2.2.3-ea9d5c42) to support-multi-dex
https://github.com/testwhat/SmaliEx/releases/download/snapshot/oat2dex.jar
https://github.com/testwhat/SmaliEx/releases/download/snapshot/baksmali.jar
https://github.com/testwhat/SmaliEx/releases/download/snapshot/smali.jar

or

This fork I've just made,
based-on oat2dex 0.90,
but using smali and baksmali latest dirty v2.4.0 source.
It has fat-jar which includes all dependencies, and docs (if that's important for some people).
https://github.com/eladkarako/SmaliEx-DirtyMod/releases

Elad Karako / September 2020.