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There is a setting which controls Automatic Publishing.
In the Servers view, right click your configuration and select Properties.
Expand the WebLogic branch in the Properties window and select the Publishing option.
Set the radio button to Never Publish Automatically
Please let us know if that works for you.
I will follow up and file a bug if necessary.
Regarding your comment "The point is that when publishing mode is set to "virtual application", then weblogic always starts up with the current version of application " is this because you assume that since the project is being deployed from the file location within the workspace, any change would have previously been deployed to the server ?
it's still possible that between two restarts of OEPE, the server was started outside OEPE and changes made via server console. While this is an edge case, it's still one that the IDE needs to be able to handle.
I will discuss your use case internally and file an enhancement/bug accordingly.
Thanks for considering my use case. You are right that I haven't considered significant portion of the deployment activity when saying "weblogic always starts up with current version", I was talking mainly about simple files which are always visible in current version to weblogic without any redeploy although eclipse thinks they need to be redeployed. Since majority of changes in our project is in simple files, I would prefer OEPE to honor Automatic Publishing setting.