fix(box): a non---rm box survives stop (keeps dir+logs) like Docker

A foreground `run` without `--rm` wiped its entire box dir (logs included) on
exit via destroy_with_options (non-persistent boxes are removed), while keeping
the state record — so the box showed in `ps -a` but `logs`/`start` found
nothing. Docker keeps a stopped container (and its logs) until `rm`.

Make a box persistent unless `--rm`: `persistent = --persistent || !--rm`.
Persistent only affects teardown cleanup (keep the box dir + overlay upper, the
overlay is unmounted either way — no mount leak); it has no boot-time effect.
`--rm` boxes and CRI pods stay non-persistent (removed on teardown, no pod-dir
leak), and `rm` force-removes regardless (cleanup_removed_box).

KVM-verified: `run` (no --rm) -> `logs` shows the output after exit and the box
is in `ps -a`; `run --rm` -> 0 boxes after; `rm` -> removed; detached logs
still complete. Completes the `run`+`logs` workflow alongside the shim-owned
log processor.

Author: Roy Lin

src/cli/src/commands/run.rs

@@ -473,7 +473,11 @@ fn build_box_config(
             vsock_port: args.sidecar_vsock_port,
             env: vec![],
         }),
-        persistent: args.common.persistent,
+        // A box without `--rm` survives its stop like a Docker stopped
+        // container: keep its dir (logs + overlay upper) so `logs`/`start` work
+        // afterwards. `--rm` boxes and CRI pods stay non-persistent (removed on
+        // teardown). `rm` force-removes either way (cleanup_removed_box).
+        persistent: args.common.persistent || !args.rm,
         ..Default::default()
     })
 }