I pushed apps into the system folders, they all got deleted by the update. Among those apps was Link2SD, which linked to all my other apps (whatever that were not in the system folder) in an external partition on my MicroSD card. The update deleted Link2SD in the system folder and broke the links.
I re-rooted, reinstalled Link2SD, and recovered most everything; but everything else I had pushed into the system folder are gone. The update basically wiped clean the system folder and set it back to the factory state with all the preinstalled craps. (I thought apps in the system folder were supposed to be able to survive a factory reset.) Fortunately I did not lose any data, but removing the bloatware (again) and reinstalling what I want will waste a lot of my time.