Generating EAR and deploying on WebSphere

We have a legacy project that was originally developed in RAD and deployed on Websphere. I am trying to get the project moved over to Intellij. After trying for couple days, I was able to generate an EAR, but was never able to deploy that EAR on the webserver. I tried taking that EAR and deploy it through the WAS admin console as well, but that did not work either. It comes back with the error saying corrupted EAR. So, now I have 2 issues.
1- GENERATE a proper Websphere deployable EAR.
When I started working on this, Intellij was complaining about the application.xml file. I manually had to create this file to get the artifact build, and I think that is part of the issue here. This is how my applicaton.xml looks like.

<application id="yRules" xmlns="http://java.sun.com/xml/ns/javaee"
             xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
             xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/application_5.xsd"
             version="5">
  <display-name>yRules.ear</display-name>
  <module id="yRules-Web">
    <web>
      <web-uri>yRules_war_new.ear</web-uri>
      <context-root>/yRules</context-root>
    </web>
  </module>

</application>


The artifact configuration attached below.

2- Deploy that EAR on Websphere.

[10/24/17 11:21:19:628 EDT] 00000001 WSChannelFram A   CHFW0019I: The Transport Channel Service has started chain SOAPAcceptorChain6.
[10/24/17 11:21:19:628 EDT] 00000001 webcontainer  I com.ibm.ws.webcontainer.WSWebContainer startChains SRVE0323I: The Asynchronous Request Dispatcher is not enabled. Requests sent through either the HttpQueueInboundDefault or the HttpQueueInboundDefaultSecure chain might not be properly handled.
[10/24/17 11:21:19:629 EDT] 00000046 SchedulerServ I   SCHD0077I: The Scheduler Service is starting the Schedulers.
[10/24/17 11:21:19:629 EDT] 00000046 SchedulerServ I   SCHD0078I: The Scheduler Service has completed starting the Schedulers.
[10/24/17 11:21:19:650 EDT] 00000001 GridConfigura I   CWLRB5873I: The GridConfiguratorMBean was activated successfully.
[10/24/17 11:21:19:655 EDT] 00000001 BatchSensorCo I   CWLRB5904I: BatchSensorComponent starting...
[10/24/17 11:21:19:708 EDT] 00000001 BatchSensorCo I   CWLRB5905I: Successfully activated GridEndpointSensorMBean.
[10/24/17 11:21:19:714 EDT] 00000001 RMIConnectorC A   ADMC0026I: The RMI Connector is available at port 2811
[10/24/17 11:21:19:718 EDT] 00000001 JMXConnectors I   ADMC0058I: The JMX JSR160RMI connector is available at port 2811
[10/24/17 11:21:19:744 EDT] 00000001 WsServerImpl  A   WSVR0001I: Server server1 open for e-business
[10/24/17 11:21:20:120 EDT] 00000045 ModelMgr      I   WSVR0801I: Initializing all server configuration models
[10/24/17 11:21:20:280 EDT] 00000045 WorkSpaceMana A   WKSP0500I: Workspace configuration consistency check is disabled.
[10/24/17 11:21:20:395 EDT] 00000064 InstallSchedu I   ADMA5016I: Installation of yRules_war_new started.
[10/24/17 11:21:20:459 EDT] 00000064 wtp           E org.eclipse.jst.j2ee.commonarchivecore.internal.impl.EARFileImpl rollUpRoles An error occurred while processing the roles in module 
    Web Module        [ org.eclipse.jst.j2ee.application.internal.impl.WebModuleImpl@3bf43612 ]
    URI               [ yRules_war_new.ear ]
    Alt DD            [ null ]
    Context Root      [ /yRules ]
 for application {location}\out\artifacts\yRules_war_new\yRules_war new.ear, error message=A file does not exist for module element having uri: yRules_war_new.ear 
[10/24/17 11:21:20:485 EDT] 00000064 FfdcProvider  W com.ibm.ws.ffdc.impl.FfdcProvider logIncident FFDC1003I: FFDC Incident emitted on C:\IBM\WebSphere\AppServer\profiles\AppSrv01\logs\ffdc\server1_97770469_17.10.24_11.21.20.4601625961995424198564.txt com.ibm.ws.management.application.task.ValidateAppTask.performTask 468
[10/24/17 11:21:20:530 EDT] 00000064 FfdcProvider  W com.ibm.ws.ffdc.impl.FfdcProvider logIncident FFDC1003I: FFDC Incident emitted on C:\IBM\WebSphere\AppServer\profiles\AppSrv01\logs\ffdc\server1_97770469_17.10.24_11.21.20.4868040751842215236436.txt com.ibm.ws.management.application.SchedulerImpl.run 328
[10/24/17 11:21:20:564 EDT] 00000064 InstallSchedu I   ADMA5014E: The installation of application yRules_war_new failed.