error: supertypes of the following classes cannot be resolved. Please make sure you have the required dependencies in the classpath

In my case I had a library module with an abstract application class implementing Dagger's HasActivityInjector and an application module with a dependency to the library and its own (non-abstract) application class extending the base app class.

My Gradle dependencies were implementations, and therefore not accessible to the application module's application class (even though there were no imports there, otherwise the issue would be immediately obvious as you'd get a 'could not resolve' error. The fix was to replace dagger implementation dependencies with api, that makes them available to dependant modules as well.

I fixed it by changing the order of plugins call!

build.gradle

buildscript {
    ext.android_plugin_version = '2.3.3'
    ext.kotlin_version = '1.1.3-2'

    repositories {
        jcenter()
        mavenCentral()

        maven { url "https://maven.google.com" }
        maven { url 'https://maven.fabric.io/public' }
        maven { url "https://jitpack.io" }
    }

    dependencies {
        classpath "com.android.tools.build:gradle:$android_plugin_version"
        classpath "org.jetbrains.kotlin:kotlin-gradle-plugin:$kotlin_version"
        classpath "org.jetbrains.kotlin:kotlin-android-extensions:$kotlin_version"
        classpath 'io.fabric.tools:gradle:1.+'
    }
}

allprojects {
    repositories {
        jcenter()
        mavenCentral()

        maven { url "https://maven.google.com" }
        maven { url 'https://maven.fabric.io/public' }
        maven { url "https://jitpack.io" }
    }
}

task clean(type: Delete) {
    delete rootProject.buildDir
}

app/build.gradle

apply plugin: 'com.android.application'
apply plugin: 'kotlin-kapt'
apply plugin: 'kotlin-android'
apply plugin: 'kotlin-android-extensions'
apply plugin: 'io.fabric'

android {
    compileSdkVersion 26
    buildToolsVersion "26.0.0"

    defaultConfig {
        applicationId "com.sample.app"
        minSdkVersion 19
        targetSdkVersion 26
        versionCode 1
        versionName "1.0.0"
        testInstrumentationRunner "android.support.test.runner.AndroidJUnitRunner"
        multiDexEnabled true
    }

    buildTypes {
        debug {
            ext.alwaysUpdateBuildId = false
        }

        release {
            minifyEnabled false
            proguardFiles getDefaultProguardFile('proguard-android.txt'), 'proguard-rules.pro'
        }
    }

    dexOptions {
        javaMaxHeapSize "4g"
    }

    dataBinding {
        enabled true
    }

    sourceSets {
        main.java.srcDirs += 'src/main/kotlin'
    }

    lintOptions {
        abortOnError false
        disable 'InvalidPackage'
    }
}

kapt {
    generateStubs = true
}

dependencies {
compile fileTree(dir: 'libs', include: ['*.jar'])
    androidTestCompile('com.android.support.test.espresso:espresso-core:2.2.2', {
        exclude group: 'com.android.support', module: 'support-annotations'
    })
    testCompile 'junit:junit:4.12'

    // kotlin
    kapt "com.android.databinding:compiler:$android_plugin_version"
    compile "org.jetbrains.kotlin:kotlin-stdlib-jre7:$kotlin_version"

    // android
    compile 'com.android.support:multidex:1.0.1'
    compile "com.android.support:appcompat-v7:${compat_version}"
    compile "com.android.support:design:${compat_version}"
    compile "com.android.support:cardview-v7:${compat_version}"
    compile "com.android.support:recyclerview-v7:${compat_version}"
    compile "com.android.support:gridlayout-v7:${compat_version}"
    compile "com.android.support:support-vector-drawable:${compat_version}"
    compile 'com.android.support.constraint:constraint-layout:1.0.2'
    compile "com.google.android.gms:play-services-ads:${play_services_version}"
    compile "com.google.android.gms:play-services-maps:${play_services_version}"
    compile "com.google.android.gms:play-services-gcm:${play_services_version}"
    compile 'com.google.maps.android:android-maps-utils:0.4+'

    // fabric
    compile('com.crashlytics.sdk.android:crashlytics:2.6.8@aar') {
        transitive = true;
    }

    // logger
    compile 'com.orhanobut:logger:2.1.1'

    // dexter
    compile 'com.karumi:dexter:4.1.0'

    // firebase
    compile "com.google.firebase:firebase-messaging:${firebase_version}"

    // persistence
    compile "android.arch.persistence.room:runtime:1.0.0-alpha3"
    annotationProcessor "android.arch.persistence.room:compiler:1.0.0-alpha3"

    // facebook
    compile 'com.facebook.android:facebook-android-sdk:4.+'

    // retrofit
    compile 'com.squareup.retrofit2:retrofit:2.3.0'
    compile 'com.squareup.retrofit2:converter-gson:2.3.0'

    // gson
    compile 'com.google.code.gson:gson:2.8.1'

    // jobs
    compile 'com.evernote:android-job:1.1.11'

    // chart
    compile 'com.github.PhilJay:MPAndroidChart:v3.0.1'

    // fresco
    compile 'com.facebook.fresco:fresco:1.3.0'

    // indicator
    compile 'com.github.JakeWharton:ViewPagerIndicator:2.4.1'
}