Refactor and Rebuild ODK Collect

I'm using Android Studio and able to run the code with all the default settings. However, while trying to refactor the org.odk.collect.android to org.rename.collect.android, I'm getting few errors. I have changed the google-services.json and android manifest. Can you please guide which are the files where i need to manually change the package names to re-build the project.
Thanks in advance.

What specific errors are you getting?

Mobile Screen says: ODK Collect has stopped

Android Studio - Run Logs:-

Install successfully finished in 17 s 214 ms.
$ adb shell am start -n "org.rename.collect.android/org.rename.collect.android.activities.SplashScreenActivity" -a android.intent.action.MAIN -c android.intent.category.LAUNCHER
Connected to process 32610 on device 'Nexus_5X_API_26 [emulator-5554]'.
Capturing and displaying logcat messages from application. This behavior can be disabled in the "Logcat output" section of the "Debugger" settings page.
W/zygote: Skipping duplicate class check due to unrecognized classloader
I/DynamiteModule: Considering local module com.google.android.gms.measurement.dynamite:20 and remote module com.google.android.gms.measurement.dynamite:21
    Selected remote version of com.google.android.gms.measurement.dynamite, version >= 21
V/DynamiteModule: Dynamite loader version >= 2, using loadModule2NoCrashUtils
W/ResourceType: ResTable_typeSpec entry count inconsistent: given 67, previously 69
    ResTable_typeSpec entry count inconsistent: given 5411, previously 5412
W/zygote: Skipping duplicate class check due to unrecognized classloader
I/FirebaseCrashlytics: Initializing Crashlytics 17.3.0
I/zygote: Background concurrent copying GC freed 7138(965KB) AllocSpace objects, 7(140KB) LOS objects, 65% free, 821KB/2MB, paused 6.405ms total 123.593ms
I/FirebaseInitProvider: FirebaseApp initialization successful
V/FA: App measurement collection enabled
V/FA: App measurement enabled for app package, google app id: org.rename.collect.android, 1:236700182196:android:5bf97e1f72dcb45230d9e1
I/FA: App measurement initialized, version: 34027
    To enable debug logging run: adb shell setprop log.tag.FA VERBOSE
I/FA: To enable faster debug mode event logging run:
      adb shell setprop debug.firebase.analytics.app org.rename.collect.android
D/FA: Debug-level message logging enabled
I/zygote: Background concurrent copying GC freed 9406(1003KB) AllocSpace objects, 12(240KB) LOS objects, 53% free, 1325KB/2MB, paused 19.726ms total 433.837ms
E/Mbgl-LibraryLoader: Failed to load native shared library.
    java.lang.UnsatisfiedLinkError: dalvik.system.PathClassLoader[DexPathList[[zip file "/system/framework/com.google.android.maps.jar", zip file "/data/app/org.rename.collect.android-zNzMafxDdc5Hmv9cIKprHw==/base.apk"],nativeLibraryDirectories=[/data/app/org.rename.collect.android-zNzMafxDdc5Hmv9cIKprHw==/lib/x86, /data/app/org.rename.collect.android-zNzMafxDdc5Hmv9cIKprHw==/base.apk!/lib/x86, /system/lib, /vendor/lib]]] couldn't find "libmapbox-gl.so"
        at java.lang.Runtime.loadLibrary0(Runtime.java:1011)
        at java.lang.System.loadLibrary(System.java:1657)
        at com.mapbox.mapboxsdk.module.loader.LibraryLoaderProviderImpl$SystemLibraryLoader.load(LibraryLoaderProviderImpl.java:29)
        at com.mapbox.mapboxsdk.LibraryLoader.load(LibraryLoader.java:43)
        at com.mapbox.mapboxsdk.net.NativeConnectivityListener.<clinit>(NativeConnectivityListener.java:13)
        at com.mapbox.mapboxsdk.net.ConnectivityReceiver.instance(ConnectivityReceiver.java:43)
        at com.mapbox.mapboxsdk.Mapbox.getInstance(Mapbox.java:67)
        at org.rename.collect.android.geo.MapboxUtils.initMapbox(MapboxUtils.java:25)
        at org.rename.collect.android.application.initialization.ApplicationInitializer.initializeMapFrameworks(ApplicationInitializer.java:125)
        at org.rename.collect.android.application.initialization.ApplicationInitializer.initializeFrameworks(ApplicationInitializer.java:71)
        at org.rename.collect.android.application.initialization.ApplicationInitializer.initialize(ApplicationInitializer.java:58)
        at org.rename.collect.android.application.Collect.onCreate(Collect.java:122)
        at android.app.Instrumentation.callApplicationOnCreate(Instrumentation.java:1118)
        at android.app.ActivityThread.handleBindApplication(ActivityThread.java:5791)
        at android.app.ActivityThread.-wrap1(Unknown Source:0)
        at android.app.ActivityThread$H.handleMessage(ActivityThread.java:1661)
        at android.os.Handler.dispatchMessage(Handler.java:105)
        at android.os.Looper.loop(Looper.java:164)
        at android.app.ActivityThread.main(ActivityThread.java:6541)
        at java.lang.reflect.Method.invoke(Native Method)
        at com.android.internal.os.Zygote$MethodAndArgsCaller.run(Zygote.java:240)
        at com.android.internal.os.ZygoteInit.main(ZygoteInit.java:767)
E/zygote: No implementation found for void com.mapbox.mapboxsdk.net.NativeConnectivityListener.initialize() (tried Java_com_mapbox_mapboxsdk_net_NativeConnectivityListener_initialize and Java_com_mapbox_mapboxsdk_net_NativeConnectivityListener_initialize__)
I/zygote: Do partial code cache collection, code=29KB, data=25KB
    After code cache collection, code=27KB, data=24KB
    Increasing code cache capacity to 128KB
I/PropertyManager: java.lang.SecurityException: getLine1NumberForDisplay: Neither user 10101 nor current process hasandroid.permission.READ_PHONE_STATE, android.permission.READ_SMS, or android.permission.READ_PHONE_NUMBERS
        at android.os.Parcel.readException(Parcel.java:1942)
        at android.os.Parcel.readException(Parcel.java:1888)
        at com.android.internal.telephony.ITelephony$Stub$Proxy.getLine1NumberForDisplay(ITelephony.java:4327)
        at android.telephony.TelephonyManager.getLine1Number(TelephonyManager.java:2402)
        at android.telephony.TelephonyManager.getLine1Number(TelephonyManager.java:2380)
        at org.rename.collect.android.injection.config.AppDependencyModule$1.getLine1Number(AppDependencyModule.java:260)
        at org.rename.collect.android.logic.PropertyManager.reload(PropertyManager.java:95)
        at org.rename.collect.android.application.initialization.ApplicationInitializer.initializeJavaRosa(ApplicationInitializer.java:86)
        at org.rename.collect.android.application.initialization.ApplicationInitializer.initializeFrameworks(ApplicationInitializer.java:72)
        at org.rename.collect.android.application.initialization.ApplicationInitializer.initialize(ApplicationInitializer.java:58)
        at org.rename.collect.android.application.Collect.onCreate(Collect.java:122)
        at android.app.Instrumentation.callApplicationOnCreate(Instrumentation.java:1118)
        at android.app.ActivityThread.handleBindApplication(ActivityThread.java:5791)
        at android.app.ActivityThread.-wrap1(Unknown Source:0)
        at android.app.ActivityThread$H.handleMessage(ActivityThread.java:1661)
        at android.os.Handler.dispatchMessage(Handler.java:105)
        at android.os.Looper.loop(Looper.java:164)
        at android.app.ActivityThread.main(ActivityThread.java:6541)
        at java.lang.reflect.Method.invoke(Native Method)
        at com.android.internal.os.Zygote$MethodAndArgsCaller.run(Zygote.java:240)
        at com.android.internal.os.ZygoteInit.main(ZygoteInit.java:767)
V/FA: Connecting to remote service
W/System.err: SLF4J: No SLF4J providers were found.
    SLF4J: Defaulting to no-operation (NOP) logger implementation
    SLF4J: See http://www.slf4j.org/codes.html#noProviders for further details.
V/FA: Detected application was in foreground
V/FA: Session started, time: 70822895
**D/AndroidRuntime: Shutting down VM**
**E/AndroidRuntime: FATAL EXCEPTION: main**
    Process: org.rename.collect.android, PID: 32610
    ***java.lang.RuntimeException: Unable to create application*** org.rename.collect.android.application.Collect: org.javarosa.core.util.externalizable.CannotCreateObjectException: org.odk.collect.android.logic.actions.setgeopoint.CollectSetGeopointAction: not found
        at android.app.ActivityThread.handleBindApplication(ActivityThread.java:5794)
        at android.app.ActivityThread.-wrap1(Unknown Source:0)
        at android.app.ActivityThread$H.handleMessage(ActivityThread.java:1661)
        at android.os.Handler.dispatchMessage(Handler.java:105)
        at android.os.Looper.loop(Looper.java:164)
        at android.app.ActivityThread.main(ActivityThread.java:6541)
        at java.lang.reflect.Method.invoke(Native Method)
        at com.android.internal.os.Zygote$MethodAndArgsCaller.run(Zygote.java:240)
        at com.android.internal.os.ZygoteInit.main(ZygoteInit.java:767)
     Caused by: org.javarosa.core.util.externalizable.CannotCreateObjectException: org.odk.collect.android.logic.actions.setgeopoint.CollectSetGeopointAction: not found
        at org.javarosa.core.services.PrototypeManager.registerPrototype(PrototypeManager.java:19)
        at org.rename.collect.android.application.initialization.ApplicationInitializer.initializeJavaRosa(ApplicationInitializer.java:96)
        at org.rename.collect.android.application.initialization.ApplicationInitializer.initializeFrameworks(ApplicationInitializer.java:72)
        at org.rename.collect.android.application.initialization.ApplicationInitializer.initialize(ApplicationInitializer.java:58)
        at org.rename.collect.android.application.Collect.onCreate(Collect.java:122)
        at android.app.Instrumentation.callApplicationOnCreate(Instrumentation.java:1118)
        at android.app.ActivityThread.handleBindApplication(ActivityThread.java:5791)
        at android.app.ActivityThread.-wrap1(Unknown Source:0) 
        at android.app.ActivityThread$H.handleMessage(ActivityThread.java:1661) 
        at android.os.Handler.dispatchMessage(Handler.java:105) 
        at android.os.Looper.loop(Looper.java:164) 
        at android.app.ActivityThread.main(ActivityThread.java:6541) 
        at java.lang.reflect.Method.invoke(Native Method) 
        at com.android.internal.os.Zygote$MethodAndArgsCaller.run(Zygote.java:240) 
        at com.android.internal.os.ZygoteInit.main(ZygoteInit.java:767) 
V/FA: Connection attempt already in progress
I/FA: Tag Manager is not found and thus will not be used
V/FA: Connection attempt already in progress
I/chatty: uid=10101(u0_a101) Measurement Wor identical 1 line
V/FA: Connection attempt already in progress
D/FA: Setting app measurement enabled (FE): true
D/FA: Updating Scion state (FE)
V/FA: Connection attempt already in progress
E/zygote: No implementation found for void com.mapbox.mapboxsdk.net.NativeConnectivityListener.finalize() (tried Java_com_mapbox_mapboxsdk_net_NativeConnectivityListener_finalize and Java_com_mapbox_mapboxsdk_net_NativeConnectivityListener_finalize__)
E/System: Uncaught exception thrown by finalizer
E/System: java.lang.UnsatisfiedLinkError: No implementation found for void com.mapbox.mapboxsdk.net.NativeConnectivityListener.finalize() (tried Java_com_mapbox_mapboxsdk_net_NativeConnectivityListener_finalize and Java_com_mapbox_mapboxsdk_net_NativeConnectivityListener_finalize__)
        at com.mapbox.mapboxsdk.net.NativeConnectivityListener.finalize(Native Method)
        at java.lang.Daemons$FinalizerDaemon.doFinalize(Daemons.java:250)
        at java.lang.Daemons$FinalizerDaemon.runInternal(Daemons.java:237)
        at java.lang.Daemons$Daemon.run(Daemons.java:103)
        at java.lang.Thread.run(Thread.java:764)

How to update the code path on the classes for re-building the ODK Collect App. Please guide.

The references you're changing in AndroidManifest.xml point to real classes in the code. If you change the references but not the actual classes they'll fail to load: ***java.lang.RuntimeException: Unable to create application*** org.rename.collect.android.application.Collect.

You should be able to rename the packages Android Studio's rename refactor, but I think it'd be a good idea to read Android's docs on app structure.

I was able to resolve the issue by replacing manually the package name.

Thanks for the help.