How to extract applications as IPA files on iOS9? As of iOS9 Apple stopped allowing iTunes or any other application to backup apps to IPA files. When it comes time to do a restore, one must download all apps. This can either be done to iTunes or on the iOS device itself. The reason is because in iOS9 apps are "thinned" so that data only necessary for an iPad does not waste storage space on an iPhone.

Tools like iTools and iMazing and CopyTrans used to offer the functionality to backup apps to IPA, but have not added support for iOS9.

To question, how to backup apps to IPA so that they can be restored without downloading them again?
If you are jailbroken, there is a solution that can be batch scripted. 

Install sbutils and ipainstaller from cydia 

ssh to phone and run these commands:

sbbundleids &gt; backup.txt
while read line; do
ipainstaller -b $line
done &lt; backup.txt

and then to install the apps:

ipainstaller *.ipa

I tested a few and it allows to upgrade apps directly from app store without fuss. (same appleid, obviously)