IntelliJ Websphere Liberty adding additional application tag to server.xml

When trying to use IntelliJ to run a spring application on Websphere Liberty Profile, when choosing to build an EAR file, my existing server.xml is updated to include an additional application tag (ending up w/ 2 tags). Ultimately, the server fails to start because it can't find missing properties files that are added to the class path and noted as such in the server.xml. This exact same project runs and deploys just fine in Eclipse using Liberty.