We may require to repack an apk for the various reasons. One of the most common being to bypass SSL Pinning.

Source: https://reverseengineering.stackexchange.com/questions/8044/repackaging-apk-file-using-baksmali-and-smali

• #!/bin/bash -e
  if ! [ "$1" ]; then
      echo "usage: $0 <file.apk>"
      exit -1
  fi
  
  fn=${1%.apk}
  target_apk=$fn.apk
  apktool d -f "$target_apk" -o smali
  echo "Done."
  

• compile-apk

  #!/bin/bash -e
  if ! [ "$1" ]; then
      echo "usage: $0 <original.apk>"
      exit -1
  fi
  
  fn=${1%.apk}
  
  rm -f $fn.unaligned.apk $fn.smali.apk
  rm -rf smali/build
  
  apktool b -f smali/ -o $fn.unaligned.apk
  jarsigner -verbose -sigalg MD5withRSA -digestalg SHA1 -keystore ~/.android/debug.keystore  -storepass android  $fn.unaligned.apk  androiddebugkey
  zipalign -v 4 $fn.unaligned.apk $fn.smali.apk
  rm -rf smali/build
  

  Steps for manual approach

• Unzip
  $ unzip test.apk
• Baksmali
  $ baksmali classes.dex -o smaliClasses
• Smali
  $ smali smaliClasses -o classes.dex
• Zip -r
  $ zip -r test.apk AndroidManifest.xml classes.dex res/ resources.arsc
• Jarsign
  $ java -jar signapk.jar testkey.x509.pem testkey.pk8 test.apk test-patched.apk
• Zipalign
  $ zipalign -v 4 test-patched.apk final-apk.apk