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 configuration every time I clean the project.
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.
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.
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