3 files changed, 29 insertions, 16 deletions

diff --git a/src/yuzu/bootmanager.cpp b/src/yuzu/bootmanager.cpp
index bfeb16458..9ceb6c8d7 100644
--- a/src/yuzu/bootmanager.cpp
+++ b/src/yuzu/bootmanager.cpp
@@ -52,6 +52,8 @@ void EmuThread::run() {
 
     emit LoadProgress(VideoCore::LoadCallbackStage::Prepare, 0, 0);
 
+    Core::System::GetInstance().RegisterHostThread();
+
     Core::System::GetInstance().Renderer().Rasterizer().LoadDiskResources(
         stop_run, [this](VideoCore::LoadCallbackStage stage, std::size_t value, std::size_t total) {
             emit LoadProgress(stage, value, total);
@@ -65,28 +67,30 @@ void EmuThread::run() {
     bool was_active = false;
     while (!stop_run) {
         if (running) {
-            if (!was_active)
+            if (was_active) {
                 emit DebugModeLeft();
+            }
 
-            Core::System::ResultStatus result = Core::System::GetInstance().RunLoop();
+            running_guard = true;
+            Core::System::ResultStatus result = Core::System::GetInstance().Run();
             if (result != Core::System::ResultStatus::Success) {
+                running_guard = false;
                 this->SetRunning(false);
                 emit ErrorThrown(result, Core::System::GetInstance().GetStatusDetails());
             }
+            running_wait.Wait();
+            result = Core::System::GetInstance().Pause();
+            if (result != Core::System::ResultStatus::Success) {
+                running_guard = false;
+                this->SetRunning(false);
+                emit ErrorThrown(result, Core::System::GetInstance().GetStatusDetails());
+            }
+            running_guard = false;
 
-            was_active = running || exec_step;
-            if (!was_active && !stop_run)
-                emit DebugModeEntered();
-        } else if (exec_step) {
-            if (!was_active)
-                emit DebugModeLeft();
-
-            exec_step = false;
-            Core::System::GetInstance().SingleStep();
+            was_active = true;
             emit DebugModeEntered();
-            yieldCurrentThread();
-
-            was_active = false;
+        } else if (exec_step) {
+            UNIMPLEMENTED();
         } else {
             std::unique_lock lock{running_mutex};
             running_cv.wait(lock, [this] { return IsRunning() || exec_step || stop_run; });
diff --git a/src/yuzu/bootmanager.h b/src/yuzu/bootmanager.h
index 3626604ca..768568b3e 100644
--- a/src/yuzu/bootmanager.h
+++ b/src/yuzu/bootmanager.h
@@ -59,6 +59,11 @@ public:
         this->running = running;
         lock.unlock();
         running_cv.notify_all();
+        if (!running) {
+            running_wait.Set();
+            /// Wait until effectively paused
+            while (running_guard);
+        }
     }
 
     /**
@@ -84,6 +89,8 @@ private:
     std::atomic_bool stop_run{false};
     std::mutex running_mutex;
     std::condition_variable running_cv;
+    Common::Event running_wait{};
+    std::atomic_bool running_guard{false};
 
 signals:
     /**
diff --git a/src/yuzu/debugger/wait_tree.cpp b/src/yuzu/debugger/wait_tree.cpp
index c1ea25fb8..765908c5a 100644
--- a/src/yuzu/debugger/wait_tree.cpp
+++ b/src/yuzu/debugger/wait_tree.cpp
@@ -59,8 +59,10 @@ std::vector<std::unique_ptr<WaitTreeThread>> WaitTreeItem::MakeThreadItemList()
     std::size_t row = 0;
     auto add_threads = [&](const std::vector<std::shared_ptr<Kernel::Thread>>& threads) {
         for (std::size_t i = 0; i < threads.size(); ++i) {
-            item_list.push_back(std::make_unique<WaitTreeThread>(*threads[i]));
-            item_list.back()->row = row;
+            if (!threads[i]->IsHLEThread()) {
+                item_list.push_back(std::make_unique<WaitTreeThread>(*threads[i]));
+                item_list.back()->row = row;
+            }
             ++row;
         }
     };