rsync corrupted my system partition. Does anyone know why and how to recover?

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I did an rsync to a partition on a second drive (mounted symbolically linked). It seemed to go OK, but then terminal was complaining that my system partition was read-only. I tried rebooting and it no longer boots. It complains it couldn't mount /tmp/ then just stops with a black screen and cursor in the top left corner.

When I boot from a USB key there is nothing obviously chewed up. At a glance my files and folders all seem to be there. And they seem to be on my backup partition. Specifically the /etc/fstab looks good.

I found one minor error in my syntax on my backup bash, but that doesn't seem to explain this. I put -e SSH (extraneously) it wasn't meant to be over SSH and I didn't include a server. (I forgot all about --dry-run. I should have done it.) Here is the command line of interest from bash (below)

Does anyone know what this would corrupt and how to fix it?

#Now do the backup

rsync -aAXve ssh --progress --exclude={"/dev/*","/proc/*","/sys/*","/tmp/*","/run/*","/mnt/*","/media/*","/lost+found","/etc/udev/devices","/OSBack/*","/VPSBack/*","/JingleShare/*","/jstorage/*","/home/*/.cache","/home/*/.thumbnails","/home/*/.local/share/Trash","/home/*/.mozilla/firefox/*/Cache","/etc/fstab","/var/run/*","/var/lock/*","/lib/modules/*/volatile/.mounted","/var/cache/apt/archives/*","/home/joe/Dropbox/*"} /* /$BACKUP_DIR
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