app_build.gradle

def localProperties = new Properties()
def localPropertiesFile = rootProject.file('local.properties')
if (localPropertiesFile.exists()) {
    localPropertiesFile.withReader('UTF-8') { reader ->
        localProperties.load(reader)
    }
}

def flutterRoot = localProperties.getProperty('flutter.sdk')
if (flutterRoot == null) {
    throw new GradleException("Flutter SDK not found. Define location with flutter.sdk in the local.properties file.")
}

def flutterVersionCode = localProperties.getProperty('flutter.versionCode')
if (flutterVersionCode == null) {
    flutterVersionCode = '1'
}

def flutterVersionName = localProperties.getProperty('flutter.versionName')
if (flutterVersionName == null) {
    flutterVersionName = '1.0'
}

apply plugin: 'com.android.application'
apply plugin: 'kotlin-android'
apply from: "$flutterRoot/packages/flutter_tools/gradle/flutter.gradle"

def keystorePropertiesFile = rootProject.file("key.properties")
def keystoreProperties = new Properties()
keystoreProperties.load(new FileInputStream(keystorePropertiesFile))

android {
    compileSdkVersion 28

    lintOptions {
        disable 'InvalidPackage'
        checkReleaseBuilds false
    }

    defaultConfig {
        // TODO: Specify your own unique Application ID (https://developer.android.com/studio/build/application-id.html).
        applicationId "xxx"
        minSdkVersion 16
        targetSdkVersion 28
        versionCode flutterVersionCode.toInteger()
        versionName flutterVersionName
        testInstrumentationRunner "android.support.test.runner.AndroidJUnitRunner"
    }

    signingConfigs {
        release {
            keyAlias keystoreProperties['keyAlias']
            keyPassword keystoreProperties['keyPassword']
            storeFile file(keystoreProperties['storeFile'])
            storePassword keystoreProperties['storePassword']
        }
    }

    buildTypes {
        release {
            signingConfig signingConfigs.release

            minifyEnabled true
            useProguard true

            proguardFiles getDefaultProguardFile('proguard-android.txt'), 'proguard-rules.pro'
        }
    }
}

flutter {
    source '../..'
}

afterEvaluate {
    mergeReleaseJniLibFolders.doLast {
        def archTypes = ["arm-release", "arm64-release"]
        archTypes.forEach { item ->
            copy {
                from zipTree("$flutterRoot/bin/cache/artifacts/engine/android-$item/flutter.jar")
                include 'lib/*/libflutter.so'
                into "$buildDir/intermediates/jniLibs/release/"
                eachFile {
                    it.path = it.path.replaceFirst("lib/", "")
                }
            }
        }
    }
}

dependencies {
    implementation "org.jetbrains.kotlin:kotlin-stdlib-jdk7:$kotlin_version"

    implementation "com.google.firebase:firebase-core:16.0.1"
    implementation "com.google.firebase:firebase-messaging:17.1.0"

    testImplementation 'junit:junit:4.12'
    androidTestImplementation 'com.android.support.test:runner:1.0.2'
    androidTestImplementation 'com.android.support.test.espresso:espresso-core:3.0.2'
}

apply plugin: 'com.google.gms.google-services'

Hi @SPodjasek, thanks for sharing the file. Mine, for the most part, looks identical.
Here is my flutter doctor

[✓] Flutter (Channel dev, v1.5.8, on Linux, locale en_US.UTF-8)
 
[✓] Android toolchain - develop for Android devices (Android SDK version 28.0.3)
[✓] Android Studio (version 3.4)
[!] VS Code (version 1.33.1)
    ✗ Flutter extension not installed; install from
      https://marketplace.visualstudio.com/items?itemName=Dart-Code.flutter
[✓] Connected device (1 available)

I wonder what is your flutter build command? I have tried the following:

• flutter clean; flutter build appbundle on my computer still omit arm64-v8a/libflutter.so
• flutter clean; flutter build apk same result
• flutter clean; flutter build apk --target-platform=android-arm64 will have the opposite effect (armeabi-v7a/libflutter.so is missing)

Here is my intermediates directory which looks absolutely fine.

I use flutter build appbundle and it always include proper libs in output build/app/outputs/bundle/release/app.aab.

Can you switch flutter to beta channel and check there?

* What went wrong:
A problem occurred evaluating root project 'android'.
> A problem occurred configuring project ':app'.
   > Could not get unknown property 'mergeReleaseJniLibFolders' for project ':app' of type org.gradle.api.Project.

worked for me with flutter build appbundle. Thanks :D

• What went wrong:
  A problem occurred evaluating project ':app'.

Could not find method fterEvaluate() for arguments [build_8a95qgiavjx0ev0fdlftv5rhy$_run_closure4@c9821b4] on project ':app' of type
org.gradle.api.Project.

what went wrong

IMHO There's no need to use this custom app_build.gradle anymore as proper multi-arch support has landed in mainline flutter...