Websphere is a complex application server that does not behave like Tomcat, making its patching process slightly different
Resolution
There are two ways to patch Liferay Portal in Websphere, but in both ways it is very important that Websphere, along with any nodes in a cluster, is shut down completely before beginning the patching process.
Patch and Redeploy
This requires that the Patching-Tool properties file is updated to point to a Liferay Portal WAR file not deployed in Websphere, like so:
patching.mode=binary
jdk.version=jdk6
war.path=../liferay-portal-6_2-ee-sp10-20150205153520442.war/
global.lib.path=../liferay-portal-dependencies/
Once the WAR and dependencies have been patched, place the patched dependencies in Websphere and then redeploy Liferay Portal using the patched WAR
Patch the Deployed Liferay Portal Directly
This will patch the deployed Liferay Portal WAR directly hopefully avoiding any necessary steps. This method of patching may lead to issues and, if it does, it would be best to restore from backup and use the first method above
Extract the patching-tool into the AppServer directory and then run the following command in the extracted Patching-Tool directory:
patching-tool auto-discovery
A default.properties file should be created with contents that should identify the deployed Liferay Portal WAR in the installedApps directory:
patching.mode=binary
jdk.version=jdk6
war.path=../profiles/AppSrv01/installedApps/liferay-ead7385Node01Cell/liferay-portal-6_2-ee-sp10-20150205153520442_war.ear/liferay-portal-6.2-ee-sp10-20150205153520442.war/
global.lib.path=../lib/ext/
Once that has been created, you may follow the normal patching instructions for the Patching-Tool
Additional Information
For an explanation of how Websphere deploys applications in its directory structure, please review this article: Know the flow when deploying your enterprise application on WebSphere Application.
To read more about the Patching Tool in general, see this article.