PackageApplication is still here waiting for you, even if Xcode 8.3.2 excluded it, so what ?

Copy PackageApplication script to this directory /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/usr/bin , then you have to give it authority to this script ,like this chmod 777 PackageApplication

Run the following command the application will be packing to a ipa file
xcrun -sdk iphoneos PackageApplication -v youapp.app -o $(pwd)/youapp.ipa