fix(aibox): registry timeout cleanup + reader thread finalization (F2/N6+N4)

N6: both streaming-forward timeout paths (deadline hit, join(5)
expiry) previously returned early and skipped the
tool.streaming_output / tool.output_queue cleanup, leaving the daemon
thread writing through the instance attribute — zombie output could
leak into the next session's queue once the attribute got reassigned.
Now unified through a timed_out flag with cleanup at the single exit;
stream_tool_timeout becomes an instance attribute (3600s default,
test-tunable).

N4: reader-thread finalization after timeout/grace break. First
implementation followed the audit suggestion (close stdout + join),
but PoC regression proved close() blocks: CPython stream objects hold
an internal lock, so closing while readline is blocked parks until
readline returns (PoC-1 regressed 3s -> 15.2s, exactly the
Start-Sleep duration). Corrected strategy: when reader already got
EOF, close stdout to release the pipe fd; when reader is still
blocked, only join(timeout=2) then give up (daemon-bounded, thread
ends naturally when the grandchild exits and EOF arrives), keeping
the main flow prompt. Audit report updated with this correction.

Tests: new tests/test_f2_fixes.py (5 cases), PoC regression 5/5
(PoC-1/4 back to ~5s), full suite 272 passed.

aibox/subsystems/executors.py

@@ -159,6 +159,26 @@ class SubprocessCommandExecutor(CommandExecutor):
             if output_queue:
                 output_queue.put(("line", line.rstrip('\n') + "\n"))
 
+        # N4 修复（审计 2026-08-18，二次修正）：reader 线程收尾。
+        # 超时/截断/宽限到期 break 后，reader 可能仍阻塞在 readline
+        # （Windows shell=True 下孙进程持管道写端，永远等不到 EOF）。
+        # 注意：此时不能 close stdout——CPython 流对象内部有锁，
+        # readline 持锁阻塞时 close() 会一同挂起直到 readline 返回
+        # （实测命令超时被拖满整个 Start-Sleep 时长）。reader 为 daemon
+        # 线程，孙进程退出收到 EOF 后自然结束，不阻塞主流程；
+        # reader 已正常退出的场景才 close 显式释放管道 fd。
+        if reader_done.is_set():
+            try:
+                process.stdout.close()
+            except Exception:
+                pass
+        else:
+            reader.join(timeout=2)
+            if reader.is_alive():
+                self.logger.warning(
+                    "reader 线程仍阻塞在管道读取（孙进程持写端），已放弃等待，"
+                    "线程由 daemon 兜底、随管道 EOF 自然退出")
+
         return ''.join(output_chunks), timeout_occurred, truncated
 
     def execute(self, command: str, timeout: int = 30, work_dir: str = None, env: Dict = None, **kwargs) -> str: