who and when notify the thread.wait() when thread.join() is called?

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As for jdk7 for linux, you can get the answer from the source code of openjdk.

/jdk7/hotspot/src/os/linux/vm/os_linux.cpp

int ret = pthread_create(&tid, &attr, (void* (*)(void*)) java_start, thread);

static void *java_start(Thread *thread) {
  ...
  thread->run();
  return 0;
}

and when start thread in java, the thread will be instanceof JavaThread.

/jdk7/hotspot/src/share/vm/runtime/thread.cpp

void JavaThread::run() {
  ...
  thread_main_inner();
}

void JavaThread::thread_main_inner() {
  ...
  this->exit(false);
  delete this;
}

void JavaThread::exit(bool destroy_vm, ExitType exit_type) {
  ...
  // Notify waiters on thread object. This has to be done after exit() is called
  // on the thread (if the thread is the last thread in a daemon ThreadGroup the
  // group should have the destroyed bit set before waiters are notified).
  ensure_join(this);
  ...
}

static void ensure_join(JavaThread* thread) {
  // We do not need to grap the Threads_lock, since we are operating on ourself.
  Handle threadObj(thread, thread->threadObj());
  assert(threadObj.not_null(), "java thread object must exist");
  ObjectLocker lock(threadObj, thread);
  // Ignore pending exception (ThreadDeath), since we are exiting anyway
  thread->clear_pending_exception();
  // Thread is exiting. So set thread_status field in  java.lang.Thread class to TERMINATED.
  java_lang_Thread::set_thread_status(threadObj(), java_lang_Thread::TERMINATED);
  // Clear the native thread instance - this makes isAlive return false and allows the join()
  // to complete once we've done the notify_all below
  java_lang_Thread::set_thread(threadObj(), NULL);
  lock.notify_all(thread);
  // Ignore pending exception (ThreadDeath), since we are exiting anyway
  thread->clear_pending_exception();
}

so lock.notify_all(thread) will notify all threads whose wait for the thread to finish.

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