We have deprecated integration on MoEngage SDK via Manifest configuration/tags.
In the latest integration, you need to initialize the SDK in the onCreate() of the application class of your app. Below are the metadata flags you need to remove and equivalent APIs you need to call in the onCreate() of your application class.
If you are already initializing the SDK via code in your Application class you can ignore this.

Adding App Id

Then

<!-- MANDATORY FIELD: APP ID AS SEEN ON MOENGAGE DASHBOARD APP SETTINGS PAGE -->
<meta-data
    android:name="APP_ID"
    android:value="XXXXXXXXX" />

Now

// this is the instance of the application class and "XXXXXXXXXXX" is the Workspace ID from the dashboard.
MoEngage moEngage = new MoEngage.Builder(this, "XXXXXXXXXXX")
            .build();
MoEngage.initialise(moEngage);

Adding Lifecycle Callbacks

Then

MoEHelper.getInstance(getApplicationContext()).autoIntegrate(this);

Now

Remove the above line from your Application class.

Adding meta tags to manifest for push notifications

Then

<!-- MANDATORY FIELD: SENDER ID , i.e. THE PROJECT NUMBER AS MENTIONED ON GOOGLE CLOUD CONSOLE PROJECTS PAGE -->
<meta-data
    android:name="SENDER_ID"
    android:value="id:XXXXXXXXXXXX" />

<!-- MANDATORY FIELD: THE NOTIFICATION SMALL ICON WHICH WILL BE USED TO SET TO NOTIFICATIONS POSTED -->
<meta-data
    android:name="NOTIFICATION_ICON"
    android:value="@drawable/ic_launcher" />

<!-- MANDATORY FIELD: THE NOTIFICATION LARGE ICON WHICH WILL BE USED TO SET TO NOTIFICATIONS POSTED -->
<meta-data
   android:name="NOTIFICATION_LARGE_ICON"
   android:value="@drawable/large_icon" />

Now

MoEngage moEngage =
        new MoEngage.Builder(this, "XXXXXXXXXX")
            .setSenderId("xxxxxxx") // required only if you are using GCM.
            .setNotificationSmallIcon(R.drawable.icon)
            .setNotificationLargeIcon(R.drawable.ic_launcher)
            .build();
MoEngage.initialise(moEngage);

Adding meta tags to Skip GCM Registration

Then

<meta-data
    android:name="SKIP_GCM_REGISTRATION"
    android:value="true" />

Now

        new MoEngage.Builder(this, "XXXXXXXXXX")
            .setSenderId("xxxxxxx") // required only if you are using GCM.
            .setNotificationSmallIcon(R.drawable.icon)
            .setNotificationLargeIcon(R.drawable.ic_launcher)
            .optOutTokenRegistration()
            .build();
MoEngage.initialise(moEngage);

Showing Multiple Notifications at one go

Then

<!-- OPTIONAL FIELD: THE NOTIFICATION TYPE WHICH WILL BE USED, SINGLE OR MULTIPLE. DEFAULT BEHAVIOR IS SINGLE -->
<meta-data
    android:name="NOTIFICATION_TYPE"
    android:value="@integer/notification_type_multiple" />

Now

MoEngage moEngage =
        new MoEngage.Builder(this, "XXXXXXXXXX")
            .setSenderId("xxxxxxx") // required only if you are using GCM.
            .setNotificationSmallIcon(R.drawable.icon)
            .setNotificationLargeIcon(R.drawable.ic_launcher)
            .setNotificationType(R.integer.notification_type_multiple)
            .build();
MoEngage.initialise(moEngage);

Setting notification Color

Then

<color name="moe_notification_color">[hex code of color]</color>

Now

MoEngage moEngage =
        new MoEngage.Builder(this, "XXXXXXXXXX")
            .setSenderId("xxxxxxx") // required only if you are using GCM.
            .setNotificationSmallIcon(R.drawable.icon)
            .setNotificationLargeIcon(R.drawable.ic_launcher)
            .setNotificationColor(R.color.colorAccent)
            .build();
MoEngage.initialise(moEngage);

Opt-out BackStack creation for Notification

Then

PushManager.getInstance().optoutBackStackBuilder(true);

Now

    MoEngage moEngage =
        new MoEngage.Builder(this, "XXXXXXXXX")
            .optOutBackStackBuilder()
            .build();
    MoEngage.initialise(moEngage);

Opt-out activity tracking

Then

<activity
    android:name=".SplashScreen"
    android:label="@string/app_name">
    <intent-filter>
        <action android:name="android.intent.action.MAIN" />
        <category android:name="android.intent.category.LAUNCHER" />
    </intent-filter>
    <meta-data
        android:name="OPT_OUT_TRACKING"
        android:value="true"/>
</activity>

Now

ArrayList<Class> trackingOptOut = new ArrayList<>();
trackingOptOut.add(SettingsActivity.class);

MoEngage moEngage =
    new MoEngage.Builder(this, "XXXXXXXXXXX")
        .setTrackingOptOut(trackingOptOut)
        .build();
MoEngage.initialise(moEngage);

Opt-out NavBar

Then

InAppManager.getInstance().optOutNavBar(this,true);

Now

    MoEngage moEngage =
        new MoEngage.Builder(this, "XXXXXXXXXX")
            .optOutNavBar()
            .build();
    MoEngage.initialise(moEngage);

Opt-out Activity from showing InApp

Then

<activity
 android:name="[your_activity]">
  <meta-data
    android:name="showInApp"
    android:value="false" />
</activity>

Now

ArrayList<Class> inAppOptOut = new ArrayList<>();
inAppOptOut.add(MainActivity.class);
MoEngage moEngage =
    new MoEngage.Builder(this, "XXXXXXXXXX")
        .setInAppOptOut(inAppOptOut)
        .build();
MoEngage.initialise(moEngage);

Opt-out of MoEngage extras in Deeplink

Then

PushManager.getInstance().optOutMoEngageExtras(true);

Now

    MoEngage moEngage =
        new MoEngage.Builder(this, "XXXXXXXXXXXX")
            .optOutMoEngageExtras()
            .build();
    MoEngage.initialise(moEngage);