Error Upgrading ADF App to 12c

I have a relatively new ADF application I'm working on.  I started in JDeveloper 11g R2, 11.1.2.4.0.  Everything works fine in 11g and with the recent release of JDeveloper 12c, we figured since this isn't a production app yet, we might as well upgrade.  So I opened my workspace in JDeveloper 12c, 12.1.2.0.0, and on opening the project it went through the project migration wizard, which ran without problems.  The problem is when trying to run my app, I get a deployment error.  I've tried running the application by right clicking on my main jspx and choosing "Run" (which is how I've always run locally), and also by choosing Application - Deploy - to InegratedWebLogicServer.
Here is the error I am getting on Deploy:
[01:36:29 PM] Deploying Application...
[01:37:54 PM] [Deployer:149192]Operation "deploy" on application "app" is in progress on "DefaultServer".
[01:38:02 PM] [Deployer:149192]Operation "deploy" on application "app" is in progress on "DefaultServer".
[01:38:04 PM] [Deployer:149034]An exception occurred for task [Deployer:149026]deploy application app on DefaultServer.: java.lang.ClassCastException: oracle.adf.share.jsp.ADFLibUtils cannot be cast to oracle.adf.library.webapp.LibraryUtils.
[01:38:04 PM] [Deployer:149193]Operation "deploy" on application "app" has failed on "DefaultServer".
[01:38:04 PM] weblogic.application.ModuleException: java.lang.ClassCastException: oracle.adf.share.jsp.ADFLibUtils cannot be cast to oracle.adf.library.webapp.LibraryUtils
[01:38:05 PM] Deployment cancelled.
[01:38:05 PM] ----  Deployment incomplete  ----.
[01:38:05 PM] Remote deployment failed (oracle.jdevimpl.deploy.common.Jsr88RemoteDeployer)
And here is the full stack:
####<Sep 11, 2013 1:38:04 PM EDT> <Error> <Deployer> <scottw-vbx-win7> <DefaultServer> <[ACTIVE] ExecuteThread: '2' for queue: 'weblogic.kernel.Default (self-tuning)'> <<WLS Kernel>> <> <24357ef5-1754-474a-a5d2-4aa0837f3696-00000053> <1378921084821> <BEA-149202> <Encountered an exception while attempting to commit the 1 task for the application "app".>
####<Sep 11, 2013 1:38:04 PM EDT> <Warning> <Deployer> <scottw-vbx-win7> <DefaultServer> <[ACTIVE] ExecuteThread: '14' for queue: 'weblogic.kernel.Default (self-tuning)'> <<WLS Kernel>> <> <24357ef5-1754-474a-a5d2-4aa0837f3696-00000065> <1378921084841> <BEA-149004> <Failures were detected while initiating deploy task for application "app".>
####<Sep 11, 2013 1:38:04 PM EDT> <Warning> <Deployer> <scottw-vbx-win7> <DefaultServer> <[ACTIVE] ExecuteThread: '14' for queue: 'weblogic.kernel.Default (self-tuning)'> <<WLS Kernel>> <> <24357ef5-1754-474a-a5d2-4aa0837f3696-00000065> <1378921084842> <BEA-149078> <Stack trace for message 149004
weblogic.application.ModuleException: java.lang.ClassCastException: oracle.adf.share.jsp.ADFLibUtils cannot be cast to oracle.adf.library.webapp.LibraryUtils
  at weblogic.application.internal.ExtensibleModuleWrapper.start(ExtensibleModuleWrapper.java:140)
  at weblogic.application.internal.flow.ModuleListenerInvoker.start(ModuleListenerInvoker.java:124)
  at weblogic.application.internal.flow.ModuleStateDriver$3.next(ModuleStateDriver.java:213)
  at weblogic.application.internal.flow.ModuleStateDriver$3.next(ModuleStateDriver.java:208)
  at weblogic.application.utils.StateMachineDriver.nextState(StateMachineDriver.java:42)
  at weblogic.application.internal.flow.ModuleStateDriver.start(ModuleStateDriver.java:70)
  at weblogic.application.internal.flow.StartModulesFlow.activate(StartModulesFlow.java:24)
  at weblogic.application.internal.BaseDeployment$2.next(BaseDeployment.java:729)
  at weblogic.application.utils.StateMachineDriver.nextState(StateMachineDriver.java:42)
  at weblogic.application.internal.BaseDeployment.activate(BaseDeployment.java:258)
  at weblogic.application.internal.EarDeployment.activate(EarDeployment.java:61)
  at weblogic.application.internal.DeploymentStateChecker.activate(DeploymentStateChecker.java:165)
  at weblogic.deploy.internal.targetserver.AppContainerInvoker.activate(AppContainerInvoker.java:80)
  at weblogic.deploy.internal.targetserver.operations.AbstractOperation.activate(AbstractOperation.java:586)
  at weblogic.deploy.internal.targetserver.operations.ActivateOperation.activateDeployment(ActivateOperation.java:148)
  at weblogic.deploy.internal.targetserver.operations.ActivateOperation.doCommit(ActivateOperation.java:114)
  at weblogic.deploy.internal.targetserver.operations.AbstractOperation.commit(AbstractOperation.java:339)
  at weblogic.deploy.internal.targetserver.DeploymentManager.handleDeploymentCommit(DeploymentManager.java:846)
  at weblogic.deploy.internal.targetserver.DeploymentManager.activateDeploymentList(DeploymentManager.java:1275)
  at weblogic.deploy.internal.targetserver.DeploymentManager.handleCommit(DeploymentManager.java:442)
  at weblogic.deploy.internal.targetserver.DeploymentServiceDispatcher.commit(DeploymentServiceDispatcher.java:176)
  at weblogic.deploy.service.internal.targetserver.DeploymentReceiverCallbackDeliverer.doCommitCallback(DeploymentReceiverCallbackDeliverer.java:195)
  at weblogic.deploy.service.internal.targetserver.DeploymentReceiverCallbackDeliverer.access$100(DeploymentReceiverCallbackDeliverer.java:13)
  at weblogic.deploy.service.internal.targetserver.DeploymentReceiverCallbackDeliverer$2.run(DeploymentReceiverCallbackDeliverer.java:68)
  at weblogic.work.SelfTuningWorkManagerImpl$WorkAdapterImpl.run(SelfTuningWorkManagerImpl.java:550)
  at weblogic.work.ExecuteThread.execute(ExecuteThread.java:295)
  at weblogic.work.ExecuteThread.run(ExecuteThread.java:254)
Caused By: java.lang.ClassCastException: oracle.adf.share.jsp.ADFLibUtils cannot be cast to oracle.adf.library.webapp.LibraryUtils
  at oracle.adf.library.webapp.LibraryFilter.init(LibraryFilter.java:120)
  at weblogic.servlet.internal.FilterManager$FilterInitAction.run(FilterManager.java:577)
  at weblogic.security.acl.internal.AuthenticatedSubject.doAs(AuthenticatedSubject.java:321)
  at weblogic.security.service.SecurityManager.runAs(SecurityManager.java:120)
  at weblogic.servlet.provider.WlsSubjectHandle.run(WlsSubjectHandle.java:57)
  at weblogic.servlet.internal.FilterManager.loadFilter(FilterManager.java:137)
  at weblogic.servlet.internal.FilterManager.preloadFilters(FilterManager.java:70)
  at weblogic.servlet.internal.FilterManager.preloadFilters(FilterManager.java:87)
  at weblogic.servlet.internal.WebAppServletContext.preloadResources(WebAppServletContext.java:1789)
  at weblogic.servlet.internal.WebAppServletContext.start(WebAppServletContext.java:2807)
  at weblogic.servlet.internal.WebAppModule.startContexts(WebAppModule.java:1661)
  at weblogic.servlet.internal.WebAppModule.start(WebAppModule.java:822)
  at weblogic.application.internal.ExtensibleModuleWrapper$StartStateChange.next(ExtensibleModuleWrapper.java:360)
  at weblogic.application.internal.ExtensibleModuleWrapper$StartStateChange.next(ExtensibleModuleWrapper.java:356)
  at weblogic.application.utils.StateMachineDriver.nextState(StateMachineDriver.java:42)
  at weblogic.application.internal.ExtensibleModuleWrapper.start(ExtensibleModuleWrapper.java:138)
  at weblogic.application.internal.flow.ModuleListenerInvoker.start(ModuleListenerInvoker.java:124)
  at weblogic.application.internal.flow.ModuleStateDriver$3.next(ModuleStateDriver.java:213)
  at weblogic.application.internal.flow.ModuleStateDriver$3.next(ModuleStateDriver.java:208)
  at weblogic.application.utils.StateMachineDriver.nextState(StateMachineDriver.java:42)
  at weblogic.application.internal.flow.ModuleStateDriver.start(ModuleStateDriver.java:70)
  at weblogic.application.internal.flow.StartModulesFlow.activate(StartModulesFlow.java:24)
  at weblogic.application.internal.BaseDeployment$2.next(BaseDeployment.java:729)
  at weblogic.application.utils.StateMachineDriver.nextState(StateMachineDriver.java:42)
  at weblogic.application.internal.BaseDeployment.activate(BaseDeployment.java:258)
  at weblogic.application.internal.EarDeployment.activate(EarDeployment.java:61)
  at weblogic.application.internal.DeploymentStateChecker.activate(DeploymentStateChecker.java:165)
  at weblogic.deploy.internal.targetserver.AppContainerInvoker.activate(AppContainerInvoker.java:80)
  at weblogic.deploy.internal.targetserver.operations.AbstractOperation.activate(AbstractOperation.java:586)
  at weblogic.deploy.internal.targetserver.operations.ActivateOperation.activateDeployment(ActivateOperation.java:148)
  at weblogic.deploy.internal.targetserver.operations.ActivateOperation.doCommit(ActivateOperation.java:114)
  at weblogic.deploy.internal.targetserver.operations.AbstractOperation.commit(AbstractOperation.java:339)
  at weblogic.deploy.internal.targetserver.DeploymentManager.handleDeploymentCommit(DeploymentManager.java:846)
  at weblogic.deploy.internal.targetserver.DeploymentManager.activateDeploymentList(DeploymentManager.java:1275)
  at weblogic.deploy.internal.targetserver.DeploymentManager.handleCommit(DeploymentManager.java:442)
  at weblogic.deploy.internal.targetserver.DeploymentServiceDispatcher.commit(DeploymentServiceDispatcher.java:176)
  at weblogic.deploy.service.internal.targetserver.DeploymentReceiverCallbackDeliverer.doCommitCallback(DeploymentReceiverCallbackDeliverer.java:195)
  at weblogic.deploy.service.internal.targetserver.DeploymentReceiverCallbackDeliverer.access$100(DeploymentReceiverCallbackDeliverer.java:13)
  at weblogic.deploy.service.internal.targetserver.DeploymentReceiverCallbackDeliverer$2.run(DeploymentReceiverCallbackDeliverer.java:68)
  at weblogic.work.SelfTuningWorkManagerImpl$WorkAdapterImpl.run(SelfTuningWorkManagerImpl.java:550)
  at weblogic.work.ExecuteThread.execute(ExecuteThread.java:295)
  at weblogic.work.ExecuteThread.run(ExecuteThread.java:254)
>

Hello Timo, thanks for your response!  Apologies for my delayed response, I started a vacation shortly after my last post.
I have compared my libraries in my app to the libraries in my sample app.  My app has all the same libraries plus the following libraries:
ADF Common Web Runtime
Oracle Page Templates
JPS Designtime
Oracle Extended Page Templates
ADF Model Runtime
ADF Faces Databinding Runtime
Because of this, I suspect the problem I'm having is related to removing prefer-web-inf-classes from my weblogic.xml file.  Is there something new which is set in 12c which would cause this error that does not cause it in 11g?  I do not explicitly set prefer-application-resources or prefer-application-packages anywhere and I can not find those settings when I search my project for those strings.  Here is the error when I add prefer-web-inf-classes back into my weblogic.xml file:
<Sep 25, 2013 1:08:05 PM EDT> <Error> <Deployer> <BEA-149265> <Failure occurred in the execution of deployment request with ID "1380128884883" for task "0". Error is: "weblogic.application.ModuleException: weblogic.utils.compiler.ToolFailureException: Neither <prefer-application-packages> nor <prefer-application-resources> can be specified when <prefer-web-inf-classes> is turned on in weblogic.xml"
weblogic.application.ModuleException: weblogic.utils.compiler.ToolFailureException: Neither <prefer-application-packages> nor <prefer-application-resources> can be specified when <prefer-web-inf-classes> is turned on in weblogic.xml
  at weblogic.servlet.internal.WebAppModule.initFilterClassLoader(WebAppModule.java:404)
  at weblogic.servlet.internal.WebAppModule.init(WebAppModule.java:260)
  at weblogic.servlet.internal.WebAppModule.init(WebAppModule.java:681)
  at weblogic.application.internal.flow.ScopedModuleDriver.init(ScopedModuleDriver.java:162)
  at weblogic.application.internal.ExtensibleModuleWrapper.init(ExtensibleModuleWrapper.java:98)
  Truncated. see log file for complete stacktrace
Caused By: weblogic.utils.compiler.ToolFailureException: Neither <prefer-application-packages> nor <prefer-application-resources> can be specified when <prefer-web-inf-classes> is turned on in weblogic.xml
  at weblogic.servlet.utils.WarUtils.configureFCL(WarUtils.java:386)
  at weblogic.servlet.internal.WebAppModule.initFilterClassLoader(WebAppModule.java:397)
  at weblogic.servlet.internal.WebAppModule.init(WebAppModule.java:260)
  at weblogic.servlet.internal.WebAppModule.init(WebAppModule.java:681)
  at weblogic.application.internal.flow.ScopedModuleDriver.init(ScopedModuleDriver.java:162)
  Truncated. see log file for complete stacktrace
>

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