AndroidManifest.xml versus AndroidManifest-main.xml in Temp/StagingArea

You can find the default manifest in the Unity installation files, the path will be different depending on your installation location/version but for example mine is C:\ProgramFiles\Unity_5.5.0\Editor\Data\PlaybackEngines\AndroidPlayer\Apk

 <?xml version="1.0" encoding="utf-8"?>
 <manifest
     xmlns:android="http://schemas.android.com/apk/res/android"
     package="com.unity3d.player"
     xmlns:tools="http://schemas.android.com/tools"
     android:installLocation="preferExternal"
     android:versionCode="1"
     android:versionName="1.0">
     <supports-screens
         android:smallScreens="true"
         android:normalScreens="true"
         android:largeScreens="true"
         android:xlargeScreens="true"
         android:anyDensity="true"/>
 
     <application
         android:theme="@style/UnityThemeSelector"
         android:icon="@drawable/app_icon"
         android:label="@string/app_name"
         android:debuggable="true">
         <activity android:name="com.unity3d.player.UnityPlayerActivity"
                   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="unityplayer.UnityActivity" android:value="true" />
         </activity>
     </application>
 </manifest>
 

Hi @MophVGX

May this might help you.

1. AndroidManifest.xml in "Temp/StaginArea" or "/Applications/Unity v5.5.1p1/PlaybackEngines/AndroidPlayer/Apk" is predefine Manifest used when developer not add it;s own Manifest in Plugins/Android folder. plus customise as per point 3

2. if developer added it's own Manifest in "Plugins/Android" Unity used that manifest for identify which activity, service ase used by game, plus make little customise as per point 3

3. It will little customise automatic for few permission like write external storage, Graphic API uses (OpenGLES 1.x / 2.x / 3.x) , bundle id, version and version code as per Player Setting we setup.

4. If you want to customise permission and few more thing for your game, then your Manifest must has at-least those items or definition maintain in "/Applications/Unity v5.5.1p1/PlaybackEngines/AndroidPlayer/Apk"

~Thanks Ranpariya Ankur {PAHeartBeat}