Cool, waiting for the fix. 

You're correct, I have had packageName specified in buildType-specific 
AndroidManifest.xml.

Look at my diff:
diff --git a/app/src/apph/AndroidManifest.xml 
b/app/src/apph/AndroidManifest.xml
index eb9275a..8f043dd 100644
--- a/app/src/apph/AndroidManifest.xml
+++ b/app/src/apph/AndroidManifest.xml
@@ -1,11 +1,10 @@
 <?xml version="1.0" encoding="utf-8"?>
 <manifest xmlns:android="http://schemas.android.com/apk/res/android";
-          xmlns:tools="http://schemas.android.com/tools";
-          package="com.myproject">
+          xmlns:tools="http://schemas.android.com/tools";>
 
     <application android:label="@string/app_name" tools:replace="label">
 
-        <activity android:name=".devopts.DevOptionsActivity" 
android:screenOrientation="portrait"/>
+        <activity android:name="com.myproject.devopts.DevOptionsActivity" 
android:screenOrientation="portrait"/>
 
         <activity
diff --git a/app/src/debug/AndroidManifest.xml 
b/app/src/debug/AndroidManifest.xml
index 71d937a..28e961f 100644
--- a/app/src/debug/AndroidManifest.xml
+++ b/app/src/debug/AndroidManifest.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="utf-8"?>
-<manifest xmlns:android="http://schemas.android.com/apk/res/android";
-          package="com.myproject">
+<manifest xmlns:android="http://schemas.android.com/apk/res/android";>
+
 
     <application>
-        <activity android:name=".devopts.DevOptionsActivity" 
android:screenOrientation="portrait"/>
+        <activity android:name="com.myproject.devopts.DevOptionsActivity" 
android:screenOrientation="portrait"/>
     </application>
 </manifest>
diff --git a/app/src/qa/AndroidManifest.xml b/app/src/qa/AndroidManifest.xml
index 80dc3fd..35946aa 100644
--- a/app/src/qa/AndroidManifest.xml
+++ b/app/src/qa/AndroidManifest.xml
@@ -1,7 +1,6 @@
 <?xml version="1.0" encoding="utf-8"?>
 <manifest xmlns:android="http://schemas.android.com/apk/res/android";
-          xmlns:tools="http://schemas.android.com/tools";
-          package="com.myproject">
+          xmlns:tools="http://schemas.android.com/tools";>
 
     <application android:label="@string/app_name" tools:replace="label">

diff --git a/build.gradle b/build.gradle
index 4fd53f3..150ffec 100644
--- a/build.gradle
+++ b/build.gradle
@@ -3,7 +3,7 @@ buildscript {
         mavenCentral()
     }
     dependencies {
-        classpath 'com.android.tools.build:gradle:0.11.+'
+        classpath 'com.android.tools.build:gradle:0.12.+'
         classpath 'org.ajoberstar:gradle-git:0.8.0'
     }
 }

Now, I have only packageName specified in my main AndroidManifest.xml file:

↪  grep -ri "package=" . --include "AndroidManifest.xml"
./src/main/AndroidManifest.xml:          package="com.myproject">

I also use applicationIdSuffix in my build.gradle:
[16:36:28] in ~/d/p/i/a/app(:ecbc29c|ecbc29c|✚4)                           
                                                                            
                                                                            
                                           
↪  grep -ri -B 4 "applicationIdSuffix" .
./build.gradle-    buildTypes {
./build.gradle-        debug {
./build.gradle-            debuggable true
./build.gradle-            buildConfigField "boolean", "USE_JAVA_LOGS", 
"true"
./build.gradle:            applicationIdSuffix ".debug"
--
./build.gradle-        }
./build.gradle-        apph {
./build.gradle-            debuggable true
./build.gradle-            buildConfigField "boolean", "USE_JAVA_LOGS", 
"true"
./build.gradle:            applicationIdSuffix ".apph"

In spite of that, error still occurs:
:app:processArmMoDebugManifest
/Users/mateuszgrzechocinski/dev/myProject/app/src/debug/AndroidManifest.xml:2:1 
Error:
Attribute manifest@package value=(com.myproject) from 
AndroidManifest.xml:3:11
is also present at com.android.support:appcompat-v7:19.1.0:17:11 
value=(android.support.v7.appcompat)
Suggestion: add 'tools:replace="package"' to <manifest> element at 
AndroidManifest.xml:2:1 to override
:app:processArmMoDebugManifest FAILED

Seems like we're doing sth differently, or my setup is somehow different 
than yours.
M.

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