Added an actual implementation for yes/no dialogs on Android using Object.wait and Object.notify.

Modified NativeLibrary to display alerts in AlertDialogs rather than Toast notifications, and allow yes/no options.
Modified MainAndroid to use the new displayAlertMsg, and to return its output.

Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/NativeLibrary.java

@@ -6,6 +6,11 @@
 
 package org.dolphinemu.dolphinemu;
 
+import android.app.AlertDialog;
+import android.content.Context;
+import android.os.Handler;
+import android.os.Looper;
+import android.os.Message;
 import android.view.Surface;
 import android.widget.Toast;
 
@@ -401,18 +406,81 @@ public final class NativeLibrary
 		CacheClassesAndMethods();
 	}
 
-	public static void displayAlertMsg(final String alert)
+	private static boolean alertResult = false;
+	public static boolean displayAlertMsg(final String caption, final String text, final boolean yesNo)
 	{
-		Log.error("[NativeLibrary] Alert: " + alert);
+		Log.error("[NativeLibrary] Alert: " + text);
 		final EmulationActivity emulationActivity = sEmulationActivity.get();
-		if (emulationActivity != null)
+		boolean result = false;
+		if (emulationActivity == null)
 		{
-			emulationActivity.runOnUiThread(() -> Toast.makeText(emulationActivity, "Panic Alert: " + alert, Toast.LENGTH_LONG).show());
+			Log.warning("[NativeLibrary] EmulationActivity is null, can't do panic alert.");
 		}
 		else
 		{
-			Log.warning("[NativeLibrary] EmulationActivity is null, can't do panic toast.");
+			// Create object used for waiting.
+			final Object lock = new Object();
+			AlertDialog.Builder builder = new AlertDialog.Builder(emulationActivity)
+				.setTitle(caption)
+				.setMessage(text);
+
+			// If not yes/no dialog just have one button that dismisses modal,
+			// otherwise have a yes and no button that sets alertResult accordingly.
+			if (!yesNo)
+			{
+				builder
+					.setCancelable(false)
+					.setPositiveButton("OK", (dialog, whichButton) ->
+					{
+						dialog.dismiss();
+						synchronized (lock)
+						{
+							lock.notify();
+						}
+					});
+			}
+			else
+			{
+				alertResult = false;
+
+				builder
+					.setPositiveButton("Yes", (dialog, whichButton) ->
+					{
+						alertResult = true;
+						dialog.dismiss();
+						synchronized (lock)
+						{
+							lock.notify();
+						}
+					})
+					.setNegativeButton("No", (dialog, whichButton) ->
+					{
+						alertResult = false;
+						dialog.dismiss();
+						synchronized (lock)
+						{
+							lock.notify();
+						}
+					});
+			}
+
+			// Show the AlertDialog on the main thread.
+			emulationActivity.runOnUiThread(() -> builder.show());
+
+			// Wait for the lock to notify that it is complete.
+			synchronized (lock)
+			{
+				try
+				{
+					lock.wait();
+				}
+				catch (Exception e) { }
+			}
+
+			if (yesNo)
+				result = alertResult;
 		}
+		return result;
 	}
 
 	public static void setEmulationActivity(EmulationActivity emulationActivity)

Source/Android/jni/MainAndroid.cpp

@@ -161,12 +161,14 @@ static bool MsgAlert(const char* caption, const char* text, bool yes_no, MsgType
   g_java_vm->AttachCurrentThread(&env, NULL);
 
   // Execute the Java method.
-  env->CallStaticVoidMethod(s_jni_class, s_jni_method_alert, env->NewStringUTF(text));
+  jboolean result =
+      env->CallStaticBooleanMethod(s_jni_class, s_jni_method_alert, env->NewStringUTF(caption),
+                                   env->NewStringUTF(text), yes_no ? JNI_TRUE : JNI_FALSE);
 
   // Must be called before the current thread exits; might as well do it here.
   g_java_vm->DetachCurrentThread();
 
-  return false;
+  return result != JNI_FALSE;
 }
 
 #define DVD_BANNER_WIDTH 96
@@ -767,8 +769,8 @@ Java_org_dolphinemu_dolphinemu_NativeLibrary_CacheClassesAndMethods(JNIEnv* env,
 
   // Method signature taken from javap -s
   // Source/Android/app/build/intermediates/classes/arm/debug/org/dolphinemu/dolphinemu/NativeLibrary.class
-  s_jni_method_alert =
-      env->GetStaticMethodID(s_jni_class, "displayAlertMsg", "(Ljava/lang/String;)V");
+  s_jni_method_alert = env->GetStaticMethodID(s_jni_class, "displayAlertMsg",
+                                              "(Ljava/lang/String;Ljava/lang/String;Z)Z");
 }
 
 // Surface Handling