I can\'t seem to find this configuration at .project file. I am looking for a way to change this setting programmatically as \"I don\'t know why\" my eclipse is losing this conf
I faced the same problem and the reason being that the file .settings/org.eclipse.wst.common.component contained entries added by Git. On removing them, and restarting the eclipse worked for me.
The deployment assembly settings are stored in the file:
.settings/org.eclipse.wst.common.component
However, in a basic J2EE Eclipse install this file shouldn't be modified by cleaning the project. Maybe you have some other plugin installed that is updating the deployment settings during the build.