resign_ipa.sh

#!/bin/bash
#name of ipa file
IPA=""
#path to .mobileprovision
PROVISION="" 
#certificate name as appears in the keychain e.g. "iPHONE Distribution: Example "
CERTIFICATE="" 
#bundle identifier e.g. com.yourcompany.app
BUNDLE_ID=""
###########
unzip -q "$IPA"
# remove the signature
rm -rf Payload/*.app/_CodeSignature Payload/*.app/CodeResources

# extract plist from .mobileprovision file
security cms -D -i "$PROVISION" > ProvisionProfile.plist 2>&1
# extract entitilements.plist from plist
/usr/libexec/PlistBuddy -x -c "Print Entitlements" ProvisionProfile.plist > Entitlements.plist 2>&1

# replace the provision
cp "$PROVISION" Payload/*.app/embedded.mobileprovision

#Modify bundle identifier in Info.plist as shown in apple developer center (e.g. com.yourcompany.app). 
$(/usr/libexec/PlistBuddy -x -c 'Set :CFBundleIdentifier '$BUNDLE_ID'' Payload/elevation.app/Info.plist 
# Verify bundle_id changed correctly 
$(/usr/libexec/PlistBuddy -x -c 'Print :CFBundleIdentifier' Payload/elevation.app/Info.plist )

# sign with the new certificate
codesign -f -s "$CERTIFICATE" --entitlements Entitlements.plist Payload/*.app

zip -qr resigned.ipa Payload