How to extract applications as IPA files on iOS9?
Solution 1:
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 > backup.txt
while read line; do
ipainstaller -b $line
done < 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)