When deploying a WAR file the plugin packages it into an EAR. In order to do so it also creates an application.xml file with the module details.
One detail is the context-root of the application which is currenltly the WAR file name.
This poses problems for instance when building WAR with Maven, since the WAR name will contain the version, which on change will change the context root of the application. This in turn might break other modules or resources depending on the context root.
I opened a PR on GitHub that closes the issue (https://github.com/jenkinsci/websphere-deployer-plugin/pull/6) by reading the context root specified in the ibm-web-ext.xml file, when present.