Android: Always run HandleInit logic on app start

Note: By "HandleInit" in this commit message, I mean the code that is
in HandleInit in master except the part that launches EmulationActivity.
In other words, I mean the call to SetUserDirectory and the call to
DirectoryInitializationService.startService. Couldn't think of
something more accurate to call that than "HandleInit"...

In master, HandleInit only runs when the main activity is launched.
This is a problem if the app ends up being launched in some other way,
such as resuming EmulationActivity after the app has been killed in
order to reclaim memory. It's important that we run HandleInit, because
otherwise the native code won't know where the User and Sys folders are.

In order to implement this, I'm dropping the ability to set a custom
User folder in an intent. I don't think anyone is using that anyway.
It's not impossible to support it, but I can't see a way to support
it that doesn't involve something ugly like having code for calling
HandleInit in every activity (or at least MainActivity + TvMainActivity
+ EmulationActivity, with more activities potentially needing it in
the future if we expand the usage of native code for e.g. settings).
If we want to support setting a custom user directory, we should
consider another way to do it, such as a setting that's stored in
getFilesDir() or getExternalStorageDirectory(). Intents are intended
to control the behavior of a specific activity, not the whole app.

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

@@ -3,6 +3,8 @@ package org.dolphinemu.dolphinemu;
 import android.app.Application;
 
 import org.dolphinemu.dolphinemu.model.GameDatabase;
+import org.dolphinemu.dolphinemu.services.DirectoryInitializationService;
+import org.dolphinemu.dolphinemu.utils.PermissionsHandler;
 
 public class DolphinApplication extends Application
 {
@@ -13,6 +15,11 @@ public class DolphinApplication extends Application
 	{
 		super.onCreate();
 
+		NativeLibrary.SetUserDirectory("");  // Empty string means use the default path
+
+		if (PermissionsHandler.hasWriteAccess(getApplicationContext()))
+			DirectoryInitializationService.startService(getApplicationContext());
+
 		databaseHelper = new GameDatabase(this);
 	}
 }

Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/ui/main/MainActivity.java

@@ -58,7 +58,6 @@ public final class MainActivity extends AppCompatActivity implements MainView
 		mPresenter.onCreate();
 
 		// Stuff in this block only happens when this activity is newly created (i.e. not a rotation)
-		// TODO Split some of this stuff into Application.onCreate()
 		if (savedInstanceState == null)
 			StartupHandler.HandleInit(this);
 

Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/utils/StartupHandler.java

@@ -5,28 +5,19 @@ import android.os.Bundle;
 import android.support.v4.app.FragmentActivity;
 import android.text.TextUtils;
 
-import org.dolphinemu.dolphinemu.NativeLibrary;
 import org.dolphinemu.dolphinemu.activities.EmulationActivity;
-import org.dolphinemu.dolphinemu.services.DirectoryInitializationService;
 
 public final class StartupHandler
 {
 	public static boolean HandleInit(FragmentActivity parent)
 	{
-		String user_dir = "";
-		String start_file = "";
+		// Ask the user to grant write permission if it's not already granted
+		PermissionsHandler.checkWritePermission(parent);
 
+		String start_file = "";
 		Bundle extras = parent.getIntent().getExtras();
 		if (extras != null)
-		{
-			user_dir = extras.getString("UserDir");
 			start_file = extras.getString("AutoStartFile");
-		}
-
-		NativeLibrary.SetUserDirectory(user_dir);  // Uses default path if user_dir equals ""
-
-		if (PermissionsHandler.checkWritePermission(parent))
-			DirectoryInitializationService.startService(parent);
 
 		if (!TextUtils.isEmpty(start_file))
 		{