• build (and build directory if there are multiple modules in a project)
• .idea
• *.iml
• local.properties
• .DS_Store
• .gradle
• .cxx

Get the list of installed packages to determine what to pull:

> adb shell pm list packages | grep tom
package:com.customermobile.preload.vzw
package:com.fanqies.tomatofn

With the package name, we can get the actual file name and location of the APK using:

> adb shell pm path com.fanqies.tomatofn
package:/data/app/com.fanqies.tomatofn-g0zd0oekwgIETU7mS62UEQ==/base.apk

Then pull it:

adb pull /data/app/com.fanqies.tomatofn-g0zd0oekwgIETU7mS62UEQ==/base.apk

This will result in an APK file “base.apk” downloaded onto your computer. Rename it appropriately:

mv base.apk tomato.apk

Follow directions at https://malacupa.com/2018/11/11/debug-decompiled-smali-code-in-android-studio-3.2.html

rm -rf $1_pre.apk 
rm -rf $1_signed.apk
rm -rf %1_aligned.apk 

apktool b -o $1_pre.apk $1
~/Library/Android/sdk/build-tools/28.0.3/zipalign -f 4 $1_pre.apk $1_aligned.apk
echo "android" | ~/Library/Android/sdk/build-tools/27.0.3/apksigner sign --ks ~/.android/debug.keystore --out $1_signed.apk $1_aligned.apk 
rm -rf $1_pre.apk 
rm -rf $1_aligned.apk 

echo ""
echo -n "Signed APK: "
echo $1_signed.apk
echo ""

Then uninstall the app on the phone. Then install it from your computer:

adb install tomato_project_signed.apk