ClassNotFoundException on subsequent builds after converting MainActivity to Kotlin

I want to give Kotlin a try, so I decided to try converting one class of my project to Kotlin and see how it integrates with my workflow before trying to convert my entire project. I can build and my application is working correctly, but after every subsequent build after the first one, I get an exception from the ClassLoader class. The app only works after cleaning and it worked great before I changed anything. I can run HelloWorld project on the same machine multiple times without error. The answers in this question didn't help: ClassNotFoundException in custom style using kotlin

07-31 14:35:41.563    1878-1878/com.ddiehl.android.htn.debug
E/AndroidRuntime﹕ FATAL EXCEPTION: main
Process: com.ddiehl.android.htn.debug, PID: 1878
    java.lang.RuntimeException: Unable to instantiate activity ComponentInfo{com.ddiehl.android.htn.debug/com.ddiehl.android.htn.view.activities.MainActivity}: java.lang.ClassNotFoundException: Didn't find class "com.ddiehl.android.htn.view.activities.MainActivity" on path: DexPathList[[zip file "/data/app/com.ddiehl.android.htn.debug-1/base.apk"],nativeLibraryDirectories=[/data/app/com.ddiehl.android.htn.debug-1/lib/arm, /vendor/lib, /system/lib]]
            at android.app.ActivityThread.performLaunchActivity(ActivityThread.java:2209)
            at android.app.ActivityThread.handleLaunchActivity(ActivityThread.java:2360)
            at android.app.ActivityThread.access$800(ActivityThread.java:144)
            at android.app.ActivityThread$H.handleMessage(ActivityThread.java:1278)
            at android.os.Handler.dispatchMessage(Handler.java:102)
            at android.os.Looper.loop(Looper.java:135)
            at android.app.ActivityThread.main(ActivityThread.java:5221)
            at java.lang.reflect.Method.invoke(Native Method)
            at java.lang.reflect.Method.invoke(Method.java:372)
            at com.android.internal.os.ZygoteInit$MethodAndArgsCaller.run(ZygoteInit.java:899)
            at com.android.internal.os.ZygoteInit.main(ZygoteInit.java:694)
     Caused by: java.lang.ClassNotFoundException: Didn't find class "com.ddiehl.android.htn.view.activities.MainActivity" on path: DexPathList[[zip file "/data/app/com.ddiehl.android.htn.debug-1/base.apk"],nativeLibraryDirectories=[/data/app/com.ddiehl.android.htn.debug-1/lib/arm, /vendor/lib, /system/lib]]
            at dalvik.system.BaseDexClassLoader.findClass(BaseDexClassLoader.java:56)
            at java.lang.ClassLoader.loadClass(ClassLoader.java:511)
            at java.lang.ClassLoader.loadClass(ClassLoader.java:469)
            at android.app.Instrumentation.newActivity(Instrumentation.java:1065)
            at android.app.ActivityThread.performLaunchActivity(ActivityThread.java:2199)
            at android.app.ActivityThread.handleLaunchActivity(ActivityThread.java:2360)
            at android.app.ActivityThread.access$800(ActivityThread.java:144)
            at android.app.ActivityThread$H.handleMessage(ActivityThread.java:1278)
            at android.os.Handler.dispatchMessage(Handler.java:102)
            at android.os.Looper.loop(Looper.java:135)
            at android.app.ActivityThread.main(ActivityThread.java:5221)
            at java.lang.reflect.Method.invoke(Native Method)
            at java.lang.reflect.Method.invoke(Method.java:372)
            at com.android.internal.os.ZygoteInit$MethodAndArgsCaller.run(ZygoteInit.java:899)
            at com.android.internal.os.ZygoteInit.main(ZygoteInit.java:694)
    Suppressed: java.lang.ClassNotFoundException: com.ddiehl.android.htn.view.activities.MainActivity
            at java.lang.Class.classForName(Native Method)
            at java.lang.BootClassLoader.findClass(ClassLoader.java:781)
            at java.lang.BootClassLoader.loadClass(ClassLoader.java:841)
            at java.lang.ClassLoader.loadClass(ClassLoader.java:504)
            ... 13 more
     Caused by: java.lang.NoClassDefFoundError: Class not found using the boot class loader; no stack available

      

        
        
        
      

    

Does anyone have an idea why my app might work on the first build but not on subsequent builds? Here is my build.gradle, manifest and activity for reference.

build.gradle (app module)

apply plugin: 'com.android.application'
apply plugin: 'kotlin-android'
apply plugin: 'com.jakewharton.hugo'
apply plugin: 'com.getkeepsafe.dexcount'
apply plugin: 'me.tatarka.retrolambda'

android {
    compileSdkVersion 22
    buildToolsVersion "23 rc3"
    defaultConfig {
        applicationId "com.ddiehl.android.htn"
        minSdkVersion 15
        targetSdkVersion 22
        versionCode 4
        versionName "0.3.0-dev"
        ndk {
            moduleName "app"
        }
    }
    signingConfigs {
        release {
            storeFile file(ANDROID_KEYSTORE_PATH)
            storePassword ANDROID_KEYSTORE_PWD
            keyAlias HTN_KEYSTORE_ALIAS
            keyPassword HTN_KEYSTORE_PWD
        }
    }
    buildTypes {
        debug {
            applicationIdSuffix ".debug"
            minifyEnabled false
        }

        release {
            debuggable false
            minifyEnabled true
            proguardFiles getDefaultProguardFile('proguard-android-optimize.txt'), 'proguard-rules.pro'
            signingConfig signingConfigs.release
        }
    }
    compileOptions {
        sourceCompatibility JavaVersion.VERSION_1_8
        targetCompatibility JavaVersion.VERSION_1_8
    }
    sourceSets {
        main.java.srcDirs += 'src/main/kotlin'
        debug.java.srcDirs += 'src/debug/kotlin'
    }
}

def getLocalProperty(s) {
    Properties properties = new Properties()
    properties.load(project.rootProject.file('local.properties').newDataInputStream())
    return properties.getProperty(s)
}

retrolambda {
    jdk getLocalProperty("jdk8.dir")
}

dependencies {
    compile project(':reddit')
    compile project(':mopub')
    compile project(':flurry')
    compile "org.jetbrains.kotlin:kotlin-stdlib:$kotlin_version"
    compile 'com.android.support:appcompat-v7:22.2.1'
    compile 'com.android.support:support-v4:22.2.1'
    compile 'com.android.support:design:22.2.0'
    compile 'com.android.support:recyclerview-v7:22.2.1'
    compile 'com.android.support:cardview-v7:22.2.1'
    compile 'com.google.android.gms:play-services-ads:7.5.0'
    compile 'com.squareup.okhttp:okhttp:2.4.0'
    compile 'com.squareup.okhttp:okhttp-urlconnection:2.4.0'
    compile 'com.squareup.retrofit:retrofit:1.9.0'
    compile 'com.squareup:otto:1.3.5'
    compile 'com.squareup.picasso:picasso:2.5.2'
    compile 'com.jakewharton:butterknife:7.0.0'
    compile 'com.jakewharton:kotterknife:0.1.0-SNAPSHOT'
    compile 'io.reactivex:rxandroid:0.25.0'
    compile 'com.facebook.stetho:stetho:1.1.1'
    compile 'com.facebook.stetho:stetho-okhttp:1.1.1'
    debugCompile 'com.squareup.leakcanary:leakcanary-android:1.3.1'
    releaseCompile 'com.squareup.leakcanary:leakcanary-android-no-op:1.3.1'
}

buildscript {
    ext.kotlin_version = '0.12.1230'
    repositories {
        mavenCentral()
        maven {
            url 'http://oss.sonatype.org/content/repositories/snapshots'
        }
    }
    dependencies {
        classpath "org.jetbrains.kotlin:kotlin-gradle-plugin:$kotlin_version"
    }
}

repositories {
    mavenCentral()
    maven {
        url 'http://oss.sonatype.org/content/repositories/snapshots'
    }
}

      

        
        
        
      

    

AndroidManifest.xml

<?xml version="1.0" encoding="utf-8"?>
<manifest xmlns:android="http://schemas.android.com/apk/res/android"
    package="com.ddiehl.android.htn" >

    <uses-permission android:name="android.permission.INTERNET" />
    <uses-permission android:name="android.permission.ACCESS_NETWORK_STATE"/>
    <uses-permission android:name="android.permission.WRITE_EXTERNAL_STORAGE"/>

    <application
        android:name="com.ddiehl.android.htn.HoldTheNarwhal"
        android:allowBackup="true"
        android:icon="@mipmap/ic_launcher"
        android:label="@string/app_name"
        android:theme="@style/AppTheme"
        android:supportsRtl="true">

        <meta-data android:name="com.google.android.gms.version"
            android:value="@integer/google_play_services_version" />

        <activity
            android:name="com.ddiehl.android.htn.view.activities.MainActivity"
            android:label="@string/app_name"
            android:configChanges="keyboard|keyboardHidden|orientation|screenLayout|uiMode|screenSize|smallestScreenSize">
            <intent-filter>
                <action android:name="android.intent.action.MAIN" />

                <category android:name="android.intent.category.LAUNCHER" />
            </intent-filter>
            <intent-filter>
                <action android:name="android.intent.action.VIEW" />

                <category android:name="android.intent.category.DEFAULT" />
                <category android:name="android.intent.category.BROWSABLE" />

                <data
                    android:host="www.damiendiehl.net"
                    android:scheme="http" />
            </intent-filter>
        </activity>
    </application>

</manifest>

      

        
        
        
      

    

MainActivity.kt (I edited most of the view-related logic, it was 400 lines, and at the moment it is a closed source project. I can use the full file if needed, but if needed).

package com.ddiehl.android.htn.view.activities

import android.app.Dialog
import android.app.ProgressDialog
import android.os.AsyncTask
import android.os.Build
import android.os.Bundle
import android.support.design.widget.NavigationView
import android.support.design.widget.Snackbar
import android.support.v4.content.ContextCompat
import android.support.v4.view.GravityCompat
import android.support.v4.widget.DrawerLayout
import android.support.v7.app.AppCompatActivity
import android.support.v7.widget.Toolbar
import android.view.MenuItem
import android.view.View
import android.view.Window
import android.widget.EditText
import android.widget.ImageView
import android.widget.TextView
import butterknife.Bind
import butterknife.ButterKnife
import butterknife.OnClick
import butterknife.bindView
import com.flurry.android.FlurryAgent
import com.flurry.android.FlurryAgentListener
import com.mopub.common.MoPub
import com.mopub.mobileads.MoPubConversionTracker
import hugo.weaving.DebugLog
import java.util.HashMap
import kotlin.properties.Delegates

public class MainActivity : AppCompatActivity(), MainView, ConfirmSignOutDialog.Callbacks, NavigationView.OnNavigationItemSelectedListener {

    private val mBus = BusProvider.getInstance()
    private var mMainPresenter: MainPresenter? = null
    private var mLastAuthCode: String? = null

    private var mProgressBar: ProgressDialog? = null
    private var mSubredditNavigationDialog: Dialog? = null

    val mDrawerLayout: DrawerLayout by bindView(R.id.drawer_layout)

    private var mAccessTokenManager: AccessTokenManager? = null

    DebugLog
    override fun onCreate(savedInstanceState: Bundle?) {
        super<AppCompatActivity>.onCreate(savedInstanceState)
        setContentView(R.layout.activity_main)

        ButterKnife.bind(this@MainActivity)

        Init().execute()
    }

    private inner class Init : AsyncTask<Void, Void, Void>() {
        override fun onPreExecute() {
            super.onPreExecute()

            mNavigationView.setNavigationItemSelectedListener(this@MainActivity)

            val toolbar = ButterKnife.findById<Toolbar>(this@MainActivity, R.id.toolbar)
            setSupportActionBar(toolbar)
            val actionBar = getSupportActionBar()
            if (actionBar != null) {
                actionBar.setHomeAsUpIndicator(R.drawable.ic_navigation_menu)
                actionBar.setDisplayHomeAsUpEnabled(true)
            }
        }

        override fun doInBackground(vararg params: Void): Void? {
            mAccessTokenManager = AccessTokenManager.getInstance(this@MainActivity)
            return null
        }

        override fun onPostExecute(aVoid: Void?) {
            super.onPostExecute(aVoid)
            onAppInitialized()
        }
    }

    override fun onStart() {
        super<AppCompatActivity>.onStart()

        if (mAccessTokenManager == null) {
            showSpinner(R.string.application_loading)
        } else {
            onAppInitialized()
        }
    }

    private fun onAppInitialized() {
        mBus.register(mAccessTokenManager)

        FlurryAgent.onStartSession(this)
        dismissSpinner()
        updateUserIdentity()
        showSubredditIfEmpty(null)
    }

    override fun onStop() {
        super<AppCompatActivity>.onStop()
        FlurryAgent.onEndSession(this)
        mBus.unregister(mAccessTokenManager)
    }

    companion object {
        public val TAG: String = javaClass<MainActivity>().getSimpleName()

        private val DIALOG_CONFIRM_SIGN_OUT = "dialog_confirm_sign_out"
        private val FLURRY_SESSION_TIMEOUT_SECONDS = 30
    }

}