I found the problem and it’s really bad. Looking at your log, here’s the catastrophic command that was run:
rm -rf tests/ patches/ plan/ ~/
Not that it’s a foolproof solution, but I’ve aliased rm to a trash command for almost ten years now to move files to the trash instead of deleting them. A trash command is built into macOS Sequoia and newer.
The one downside is the command doesn’t support the -f or -r arguments, so it often causes issues with Claude Code. Sometimes it’ll switch to using rmdir, so I’m also aliasing that now.
I’m not sure how much moving the home directory to the trash would have helped, since the trash command does completely remove files and directories prefixed with a period.