# decode apk
$ apktool d base.apk
I: Using Apktool 2.6.1 on base.apk
I: Loading resource table...
I: Decoding AndroidManifest.xml with resources...
I: Loading resource table from file: ...1.apk
I: Regular manifest package...
I: Decoding file-resources...
I: Decoding values */* XMLs...
I: Baksmaling classes.dex...
I: Copying assets and libs...
I: Copying unknown files...
I: Copying original files...
I: Copying META-INF/services directory

# checkout AndroidManifest.xml

# unzip apk
$ unzip base.apk -d unzip
Archive:  base.apk
  inflating: unzip/AndroidManifest.xml

# dex to jar
$ cd unzip
$ d2j-dex2jar classes.dex
dex2jar classes.dex -> ./classes-dex2jar.jar

# build apk
$ apktool b base/ -o patched.apk
I: Using Apktool 2.6.1
I: Checking whether sources has changed...
I: Checking whether resources has changed...
I: Building apk file...
I: Copying unknown files/dir...
I: Built apk...