Android: Fix in-game settings changes not getting saved

EmulationActivity has an instance of Settings. If you go to
SettingsActivity from EmulationActivity and change some settings,
the changes get saved to disk, but EmulationActivity's Settings
instance still contains the old settings in its map of all
settings (assuming the EmulationActivity was not killed by the
system to save memory). Then, once you're done playing your
game and exit EmulationActivity, EmulationActivity calls
Settings.saveSettings. This call to saveSettings first overwrites
the entire INI file with its map of all settings (which is
outdated) in order to save any legacy settings that have changed
(which they haven't, since the GUI doesn't let you change legacy
settings while a game is running). Then, it asks the new config
system to write the most up-to-date values available for non-legacy
settings, which should make all the settings be up-to-date again.
The problem here is that the new config system would skip writing
to disk if no settings changes had been made since the last time
we asked it to write to disk (i.e. since SettingsActivity exited).

NB: Calling Settings.loadSettings in EmulationActivity.onResume
is not a working solution. I assume this is because
SettingsActivity saves its settings in onStop and not onPause.

Source/Android/jni/NativeConfig.cpp

@@ -128,7 +128,12 @@ Java_org_dolphinemu_dolphinemu_features_settings_model_NativeConfig_unloadGameIn
 JNIEXPORT void JNICALL Java_org_dolphinemu_dolphinemu_features_settings_model_NativeConfig_save(
     JNIEnv*, jclass, jint layer)
 {
-  return GetLayer(layer, {})->Save();
+  const std::shared_ptr<Config::Layer> layer_ptr = GetLayer(layer, {});
+
+  // Workaround for the Settings class carrying around a legacy map of settings it always saves
+  layer_ptr->MarkAsDirty();
+
+  return layer_ptr->Save();
 }
 
 JNIEXPORT jboolean JNICALL

Source/Core/Common/Config/Layer.h

@@ -138,6 +138,8 @@ public:
     m_map.insert_or_assign(location, std::move(new_value));
   }
 
+  void MarkAsDirty() { m_is_dirty = true; }
+
   Section GetSection(System system, const std::string& section);
   ConstSection GetSection(System system, const std::string& section) const;