I'm also finding that this is NOT fixed in 5.4.5p2 on mac, also getting the problem with merging manifests.

@JGWINNER - Thank you for this... This morning, I screwed over my ability to make Android games courtesy of another post.
@UnityTechnologies - For this issue supposedly being "Fixed" according to Unity Technologies, I sure do seem to have an issue with it not being able to build without getting the error that everyone else gets... And, in 5.6.1f, I would think that it would be fixed by now? I mean, this has been an issue since early versions of Unity 4!!!

So, add all 10 of my votes to Unity Technologies ACTUALLY fixing this issue, rather than backburner-ing it again.

hello, I am using unity5.6.1f1(64bit) for Windows 10.
I also met the merge issue.
=======================================================
Merging manifest with lower AndroidManifest.xml:2:1-8:12
Merging application with lower AndroidManifest.xml:3:3-5:17
C:\Users\kaennkyou\Documents\gearvr001\Temp\StagingArea\AndroidManifest-main.xml:4:125-150 Error:
Attribute application@debuggable value=(true) from AndroidManifest-main.xml:4:125-150
is also present at AndroidManifest.xml:3:148-174 value=(false).
Suggestion: add 'tools:replace="android:debuggable"' to <application> element at AndroidManifest-main.xml:4:3-12:17 to override.
C:\Users\kaennkyou\Documents\gearvr001\Temp\StagingArea\AndroidManifest-main.xml:4:16-57 Error:
Attribute application@theme value=(@style/UnityThemeSelector) from AndroidManifest-main.xml:4:16-57
is also present at AndroidManifest.xml:3:83-147 value=(@android:style/Theme.Black.NoTitleBar.Fullscreen).
Suggestion: add 'tools:replace="android:theme"' to <application> element at AndroidManifest-main.xml:4:3-12:17 to override.
===============================================

It is weird, it automatically create AndroidManifest-main in myproject\Temp\StagingArea\
and AndroidManifest in myproject\Temp\StagingArea\android-libraries\OVRPlugin
but in the two AndroidManifests one "application android:debuggable="false" android:theme="@android:style/Theme.Black.NoTitleBar.Fullscreen" (in OVRPlugin)
and another is <application android:debuggable="true" android:label="@string/app_name" android:icon="@drawable/app_icon" android:theme="@style/UnityThemeSelector">

they are conflicts, why to create the conflicts file I dont understand.
I tried @ JAZZPABLOMAY 10, 2017 03:59 solution, but it still does not work.
It seems it does not read the file I created in Assets/Plugins/Android.

any help will be very appreciated.
Thank you.

I can't find the "tools_r25.2.3-windows.zip" file . All i found was "sdk-tools-windows-3859397.zip".
Please help me, I don't know what to do, my unity is up to date but gives me the error "Unable to list target platforms".

It is FIXED in 5.6.0p4 !!!

I have 5.6.0p3 but still have this error. I also downloaded latest "Android SDK Tools" 26.0.2 and restart everything but still have "Error:Invalid command manifmerger". I see no other choices than try with the 2017.1.0b3 ...

The merge issue is a weird one and I found that it was to do with the way Unity is creating the manifest file in the temp folder.

Try adding this default androidManifest.xml to your project under plugins/Android remembering to change the package name and remove any unwanted permissions. The issue seems to come from there being no manifest file to actually merge with and also (when you do add the manifest) there may then be issues with some manifest files in your project (in the other libs and plugins) using incorrect icon references.

<?xml version="1.0" encoding="UTF-8"?>
<manifest xmlns:android="http://schemas.android.com/apk/res/android"
xmlns:tools="http://schemas.android.com/tools"
android:installLocation="preferExternal"
package="com.yourpackagenamehere"
android:versionName="2.0"
android:versionCode="2">
<supports-screens android:smallScreens="true" android:normalScreens="true" android:largeScreens="true" android:xlargeScreens="true" android:anyDensity="true" />
<uses-feature android:glEsVersion="0x00020000" />
<uses-sdk android:minSdkVersion="19" android:targetSdkVersion="25" />
<application android:icon="@drawable/app_icon">
<activity android:name="com.unity3d.player.UnityPlayerActivity" android:label="@string/app_name" android:configChanges="fontScale|keyboard|keyboardHidden|locale|mnc|mcc|navigation|orientation|screenLayout|screenSize|smallestScreenSize|uiMode|touchscreen" android:launchMode="singleTask" android:screenOrientation="landscape">
<meta-data android:name="unityplayer.ForwardNativeEventsToDalvik" android:value="true" />
<intent-filter>
<action android:name="android.intent.action.MAIN" />
<category android:name="android.intent.category.LAUNCHER" />
</intent-filter>
</activity>
</application>
<uses-permission android:name="android.permission.INTERNET" />
<uses-permission android:name="android.permission.VIBRATE" />
<uses-permission android:name="android.permission.GET_TASKS" />
<uses-permission android:name="android.permission.RECEIVE_BOOT_COMPLETED" />
<uses-permission android:name="android.permission.WRITE_EXTERNAL_STORAGE" />
<uses-permission android:name="android.permission.ACCESS_WIFI_STATE" />
<uses-permission android:name="com.android.vending.CHECK_LICENSE" />
</manifest>

yeah gee thanks unity devs, did you even test the fix before releasing it? I'm starting to think I should ask for a refund for my pro license, I've just spent a whole week working through unity bugs because you guys don't seem to give a toss anymore