No, I didn't change anything on the server except a LXAdmin update on June 4th.
I posted this on LXLabs forum and got some more clues:
h_t_t_p://forum.lxlabs.com/index.php?t=msg&th=5764&start=0&
It looks like I may have been hacked or the permissions were otherwise massively corrupted across the board. I'm looking at doing a clean reinstall now (actually I'm looking at moving back to shared hosting with a mysql container, as I'm realizing I don't have the stomach or the expertise to manage a VPS).
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