[Android Q&A, Help & Troubleshooting] nc1212:
After successfully compiling AOSP Marshmallow 6.0.1 I tried to install the Dialer in a stock Nexus 5X ROM of the same build number.

AOSP build: MHC19J android-6.0.1_r22 bullhead user-debug

Nexus Stock ROM build: MHC19J

I install it by pushing the Dialer and Contacts apk to /system/priv-app and assigning proper SELinux permissions

chcon u:object_r:system_file:s0

to every newly added file and folder.

After booting up, launching Dialer results in the following error:

W/System(5353): ClassLoader referenced unknown path: /system/priv-app/Dialer/lib/arm64
D/AndroidRuntime(5353): Shutting down VM
E/AndroidRuntime(5353): FATAL EXCEPTION: main
E/AndroidRuntime(5353): Process: com.android.dialer, PID: 5353
E/AndroidRuntime(5353): java.lang.RuntimeException: Unable to instantiate application com.android.dialer.DialerApplication: java.lang.ClassNotFoundException: Didn't find class "com.android.dialer.DialerApplication" on path: DexPathList[[zip file "/system/priv-app/Dialer/Dialer.apk"],nativeLibraryDirectories=[/system/priv-app/Dialer/lib/arm64, /vendor/lib64, /system/lib64]]
E/AndroidRuntime(5353): at android.app.LoadedApk.makeApplication(LoadedApk.java:578)
E/AndroidRuntime(5353): at android.app.ActivityThread.handleBindApplication(ActivityThread.java:4685)
E/AndroidRuntime(5353): at android.app.ActivityThread.-wrap1(ActivityThread.java)
E/AndroidRuntime(5353): at android.app.ActivityThread$H.handleMessage(ActivityThread.java:1405)
E/AndroidRuntime(5353): at android.os.Handler.dispatchMessage(Handler.java:102)
E/AndroidRuntime(5353): at android.os.Looper.loop(Looper.java:148)
E/AndroidRuntime(5353): at android.app.ActivityThread.main(ActivityThread.java:5422)
E/AndroidRuntime(5353): at java.lang.reflect.Method.invoke(Native Method)
E/AndroidRuntime(5353): at com.android.internal.os.ZygoteInit$MethodAndArgsCaller.run(ZygoteInit.java:726)
E/AndroidRuntime(5353): at com.android.internal.os.ZygoteInit.main(ZygoteInit.java:616)
E/AndroidRuntime(5353): Caused by: java.lang.ClassNotFoundException: Didn't find class "com.android.dialer.DialerApplication" on path: DexPathList[[zip file "/system/priv-app/Dialer/Dialer.apk"],nativeLibraryDirectories=[/system/priv-app/Dialer/lib/arm64, /vendor/lib64, /system/lib64]]
E/AndroidRuntime(5353): at dalvik.system.BaseDexClassLoader.findClass(BaseDexClassLoader.java:56)
E/AndroidRuntime(5353): at java.lang.ClassLoader.loadClass(ClassLoader.java:511)
E/AndroidRuntime(5353): at java.lang.ClassLoader.loadClass(ClassLoader.java:469)
E/AndroidRuntime(5353): at android.app.Instrumentation.newApplication(Instrumentation.java:981)
E/AndroidRuntime(5353): at android.app.LoadedApk.makeApplication(LoadedApk.java:573)
E/AndroidRuntime(5353): ... 9 more
E/AndroidRuntime(5353): Suppressed: java.io.IOException: No original dex files found for dex location /system/priv-app/Dialer/Dialer.apk
E/AndroidRuntime(5353): at dalvik.system.DexFile.openDexFileNative(Native Method)
E/AndroidRuntime(5353): at dalvik.system.DexFile.openDexFile(DexFile.java:295)
E/AndroidRuntime(5353): at dalvik.system.DexFile.<init>(DexFile.java:80)
E/AndroidRuntime(5353): at dalvik.system.DexFile.<init>(DexFile.java:59)
E/AndroidRuntime(5353): at dalvik.system.DexPathList.loadDexFile(DexPathList.java:279)
E/AndroidRuntime(5353): at dalvik.system.DexPathList.makePathElements(DexPathList.java:248)
E/AndroidRuntime(5353): at dalvik.system.DexPathList.<init>(DexPathList.java:120)
E/AndroidRuntime(5353): at dalvik.system.BaseDexClassLoader.<init>(BaseDexClassLoader.java:48)
E/AndroidRuntime(5353): at dalvik.system.PathClassLoader.<init>(PathClassLoader.java:65)
E/AndroidRuntime(5353): at android.app.ApplicationLoaders.getClassLoader(ApplicationLoaders.java:58)
E/AndroidRuntime(5353): at android.app.LoadedApk.getClassLoader(LoadedApk.java:376)
E/AndroidRuntime(5353): at android.app.LoadedApk.makeApplication(LoadedApk.java:568)
E/AndroidRuntime(5353): ... 9 more
E/AndroidRuntime(5353): Suppressed: java.lang.ClassNotFoundException: com.android.dialer.DialerApplication
E/AndroidRuntime(5353): at java.lang.Class.classForName(Native Method)
E/AndroidRuntime(5353): at java.lang.BootClassLoader.findClass(ClassLoader.java:781)
E/AndroidRuntime(5353): at java.lang.BootClassLoader.loadClass(ClassLoader.java:841)
E/AndroidRuntime(5353): at java.lang.ClassLoader.loadClass(ClassLoader.java:504)
E/AndroidRuntime(5353): ... 12 more
E/AndroidRuntime(5353): Caused by: java.lang.NoClassDefFoundError: Class not found using the boot class loader; no stack trace available

I have searched for this problem but I have only found solutions for when it is a normal Android Studio app, but nothing on AOSP.