fix: Fix race in emulator controller

[mutianf]

Fix TSan data race in EmulatorController by synchronizing logging threads.

The race condition occurred when a previous emulator process instance was shutting down
while a new instance was starting. The logging threads for stdout/stderr of the previous
process could still be reading from file descriptors that were subsequently reused for
the new process's pipes.

This fix ensures that:

1. Logging threads are tracked.
2. EmulatorController.stop() joins these threads after destroying the process.
3. EmulatorController.stop() waits for the process to exit completely.