To emphasize the answer of @Albert221, as I had confusion about what the resulting content should look like. It should be as follows.

<manifest xmlns:android="http://schemas.android.com/apk/res/android"
          xmlns:tools="http://schemas.android.com/tools">
    <!-- Added by open_filex -->
    <uses-permission android:name="android.permission.READ_MEDIA_IMAGES" tools:node="remove" />
    <uses-permission android:name="android.permission.READ_MEDIA_VIDEO" tools:node="remove" />
    <uses-permission android:name="android.permission.READ_MEDIA_AUDIO" tools:node="remove" />
    <application
        android:label="App Name"
        android:name="${applicationName}"
        android:icon="@mipmap/ic_launcher">
        <activity
        .
        .
        .
        .
    </application>
</manifest>