Ouch... for whoever is reading this, this issue is not caused just by VMWare Fusion. Today I was accessing one of our ESX servers with Safari and needed to access the console of one of the guest machines. The console popped up a VMWare-related authentication screen to install a helper app... and the same nightmare issue in this entire thread just happened to me too. By the time I realized chmod was running in the background it was too late... I’m now trying to recover the permissions.
=====update====
After trying and failing with all the methods described in this thread, this is what worked for me.
I'm using High Sierra, and as such my drive is now using APFS. With APFS Apple, if you have Time Machine enabled, creates hourly snapshots on the local drive that can then be used to restore the system state as it was before this mess. Just reboot into recovery mode (CMD-R), and select "Restore From Time Machine Backup". As the source disk, select your local disk. You'll see a list of all your hourly snapshots. Select the one you one and when the system reboots all will be back to normal.
