These are the steps that I took to redeploy my Liferay application in the Glassfish app server. I did a lot of testing and found that if you undeploy from the admin console, there are stale files left over that the app server recognizes and then it does not install Liferay as a result of existing files inside the application folder of Glassfish.
Here were the steps I took to successfully redeploy:
1. Undeploy the Liferay application from the admin console.
2. Shut down the Glassfish application server.
3. Go to the glassfish-3.1.2\domains\oneuabmed\applications directory and delete the liferay-portal application.
4. Go to the glassfish-3.1.2\domains\oneuabmed\autodeploy folder and delete both Liferay deployments within the folder. They should be named: liferay-portal.war and liferay-portal.war_deployed
5. Go to the patching-tool directory and take a look at the default.properties
6. Ensure that the properties are pointing to the right war file as well as the correct domain library path. Mine looked like this:
(It is alright to set it to a direct path for both paths, they do not have to be relative paths to the application server as long as they are set correctly.)
7. Run the patching-tool install command and check the directory /glassfish-3.1.2/domains/oneuabmed/lib to ensure that the portal-service.jar has the modified date of the day that you ran the patching-tool and also check out the liferay.war to ensure that it has the right modified date as well.
8. Turn on the application server using asadmin.bat/sh
9. Go to the Glassfish admin console.
10. Select the war file designated in the war.path from the default.properties
11. Go to the Applications -> Deploy and select the Liferay war that was patched.
12. Enter the correct context and application name, in my case I set it to the root context and called it liferay-war therefore I filled it out as "/" and "liferay-war"
13. Let it deploy completely and then see if you can bring up the portal page.