Editing AndroidManifest.xml in Gradle task processManifest.doLast has no effect when running app from Android Studio

I figured out that it's related to the Instant Run feature introduced in Android Studio 2.0. If I turn it off, everything works as expected. But since I want to use Instant Run, I digged a little further.

The thing is, with Instant Run enabled the intermediate AndroidManifest.xml file will be at another location, namely /build/intermediates/bundles/myflavor/instant-run/. That means I was effectively editing the wrong file. That other manifest file is accessible with the property instantRunManifestOutputFile, which can be used instead of manifestOutputFile.

To make it work in all use-cases I check both temporary manifest files whether they exist and modify them if so:

applicationVariants.all { variant ->
    variant.outputs.each { output ->
        output.processManifest.doLast {
            [output.processManifest.manifestOutputFile,
             output.processManifest.instantRunManifestOutputFile
            ].forEach({ File manifestOutFile ->
                if (manifestOutFile.exists()) {
                    def newFileContents = manifestOutFile.getText('UTF-8').replace("</application>", "<meta-data ... /></application>")
                    manifestOutFile.write(newFileContents, 'UTF-8')
                }
            })
        }
    }
}

There is literally no documentation of instantRunManifestOutputFile. The only Google search result I got was the Android Gradle Plugin source code. But then I also found a third potential manifest file property aaptFriendlyManifestOutputFile, which I don't know what it's about either...

I want to add some additional information to this question. The answer from @Floern is a bit outdated. The code is working on old Gradle versions. The new version of Gradle says that manifestOutputFile is deprecated and will be removed soon. instantRunManifestOutputFile doesn't exists at all. So, here is the example for the new Gradle version:

applicationVariants.all { variant ->                
    variant.outputs.each { output ->
        output.processManifest.doLast {
            def outputDirectory = output.processManifest.manifestOutputDirectory                
            File manifestOutFile = file(new File(outputDirectory, 'AndroidManifest.xml'))
            if(manifestOutFile.exists()){

                // DO WHATEVER YOU WANT WITH MANIFEST FILE. 

            }
        }
    }
}

EDIT: Here is the newer variant for Gradle 5.4.1 and Grudle plugin 3.5.1:

android.applicationVariants.all { variant -> 
    variant.outputs.each { output ->
        def processManifest = output.getProcessManifestProvider().get()
        processManifest.doLast { task ->
            def outputDir = task.getManifestOutputDirectory()
            File outputDirectory
            if (outputDir instanceof File) {
                outputDirectory = outputDir
            } else {
                outputDirectory = outputDir.get().asFile
            }
            File manifestOutFile = file("$outputDirectory/AndroidManifest.xml")

            if (manifestOutFile.exists() && manifestOutFile.canRead() && manifestOutFile.canWrite()) {

                // DO WHATEVER YOU WANT WITH MANIFEST FILE. 

            }

        }
    }
}

Hope this will help someone.