Is that cruft or past conversation history / subagent history and observability logs?

Just garbage. Temp files, worktrees that weren't removed after subagents finished, build files... all kinds of things.

But that's agent behavior, and not harness responsibility...?

Harnesses should be responsible IMO for managing lifecycle stuff, including worktrees and temp files.

It’s simple, deterministic stuff. At least most of the time.