This renames all of the files with a .smali extension to a more logical filename based on the .source entry in the smali file

apktool_name_corrector.sh

#!/bin/bash
# Renames files outputed by `apktool d <apk>` to <source>.smali where <source> is the value in the .source entry of the smali file
# This isn't meant to be 100% correct but it works in 99% of cases
# ./apktool_name_corrector.sh ~/Documents/my_smali_output_folder

shopt -s globstar
start_dir=$1

for e in "${start_dir}"/**; do
    if [ -f "${e}" ] ; then
        if [ ${e: -6} == ".smali" ] ; then
            source=$(cat "${e}" | grep -Po "(?<=\.source\s\")[^\"]*")
            dir_name=$(dirname "${e}")
            new_name="${dir_name}/${source}.smali"
            mv "${e}" "${new_name}"
        fi
    fi
done

echo "done"

If the smali output doesn't have a .source line then this is going to rename the file to .smali which is likely undesirable behavior. This should probably check that the name is not 0 length.