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`cleanup()` enumerated *every* firecracker process under the run root and *every* run dir, so `./cli.py cleanup` would kill running bottles and delete their rootfs — despite being described as orphan cleanup. The backend's `enumerate_active` registry is still a stub (#354), so there was no live/dead signal. Use the running firecracker processes themselves as that signal: a run dir with a live VM is protected (never killed, never removed); only run dirs with no live process (leaked by a hard-killed launch) are reaped, plus firecracker pids whose run dir is already gone (lingering VMMs). This makes cleanup safe to run alongside live bottles and lets it back a periodic GC for the run-dir leak the launch.py teardown fix closes on the clean-exit path. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>