Break up waiting on quit into two stages

Now that our quit event is queued, we can properly wait for it. This
way, we can separate waiting for quit and waiting for (possibly hanging)
plugins.

mainapp.cpp

@@ -962,12 +962,23 @@ void MainApp::start()
 
     oneInstanceLock.unlock();
 
-    logger->logf(LOG_DEBUG, "Waiting for threads to finish.");
+    {
+        logger->logf(LOG_DEBUG, "Waiting for our own quit event to have been queued.");
+        int count = 0;
+        while(std::any_of(threads.begin(), threads.end(), [](std::shared_ptr<ThreadData> t){ return t->running; }))
+        {
+            if (count++ >= 30000)
+                break;
+            usleep(1000);
+        }
+    }
+
+    logger->logf(LOG_DEBUG, "Waiting for threads clean-up functions to finish.");
     int count = 0;
     bool waitTimeExpired = false;
     while(std::any_of(threads.begin(), threads.end(), [](std::shared_ptr<ThreadData> t){ return !t->finished; }))
     {
-        if (count++ >= 10000)
+        if (count++ >= 30000)
         {
             waitTimeExpired = true;
             break;