Unable to open any applications Terminal System Prefs
Any time the system itself needs to be reinstalled, you can safely boot to recovery HD or internet recovery or bootable install media and then reinstall the core OS. This functions like the archive install of the old days where it sets aside your running system. Then a fresh system is installed and all users and data are migrated in to the new system.

This is super safe if you have a good backup and relatively safe even if you don't have a backup since it doesn't intentionally delete any user settings or data. You'd only lose your data and files if the system had errors anyway and that loss was just a matter of time.