So the root cause of this is similar to that of the broken Bumbeebee upgrade script [1,2]: a typo (missing quotation marks or unintended space) caused far more data than intended (a whole volume or /usr) to be rm'd.

1: https://news.ycombinator.com/item?id=2661209 2: https://github.com/MrMEEE/bumblebee-Old-and-abbandoned/commi...