There's also no point in rebuilding until he thinks the attack vector has been closed. However they got in last time, they can probably do it again.
And that is why you need to run production systems on large well supported stable distributions, like Debian, and not DudeOS or FunkyNameOS created 18 months ago by two dudes and never updated since.
FYI: I run Debian/Stable where I have a choice and stick with the provided versions of everything as a general rule, though I currently have nodejs, npm, and some related modules compiled from other sources.
Naturally these where from Chinese or Russian ip address ranges
Disclaimer: I work at a hosting company, and this is my personal experience with hacked websites.