The server I am deploying to is Weblogic 11g (10.3.5)
I created a web project and then created a seprate enterprise project. Then used the “deployment assembly” dialog to add the war project into ear project. After this I chosed “don’t modify the application.xml” which is not effective. Myeclipse is modifing the application.xml at the time of deployment
Deployment Assembly was not fully supported in MyEclipse 10.x and it had it’s limitations. With MyEclipse 2013 we have introduced full support for Deployment Assembly and better handling of applicaiton.xml, which is never rewritten, but updated only if needed (e.g. module addition through DA).
We are currently working on MyEclipse for Spring 2013, so your issue will be fixed with the next release. For now, I would recommend you to not use Deployment Assembly and manage modules through “MyEclipse” -> “Add/Remove modules” context menu of EAR project.