Eclipse plugin change in 4.4 that changes eclipse defaults - breaks execution of local server

In the release notes for gradle 4.4 it indicates that a change was made to the eclipse plugin.

The behavior we are seeing is that for java projects (java utility projects, web app projects, and ejb projects) the Allow output folders for source folders checkbox is checked and it adds “/default” to the end of the “Default output folder”.

This behavior changes the default eclipse settings. If you create any of these java projects the check box for “Allow output folders for source folders” is unchecked and the Default output folder is … projectName/bin

When this setting is applied we see class files placed into new separate folders (projectName/main/bin/default and projectName/test/bin/default), but it does not clean up the old class files in projectName/bin. This appears to confuse websphere when it is running in the eclipse workspace.

Why was this changed? Is there a way to override this behavior. We would like the old behavior that is implemented in Gradle 4.3.

The output folder separation is required by the Eclipse platform to support classpath separation between main and test sources. If you don’t need this feature you can remove the related metadata with the following snippet:

eclipse.classpath.file.whenMerged {
    entries.findAll { it instanceof org.gradle.plugins.ide.eclipse.model.SourceFolder }.each { it.entryAttributes.remove("gradle_used_by_scope"); it.entryAttributes.remove("gradle_scope"); it.entryAttributes.remove("test"); it.output = "bin/default" }
    entries.findAll { it instanceof org.gradle.plugins.ide.eclipse.model.Library }.each { it.entryAttributes.remove("gradle_used_by_scope"); it.entryAttributes.remove("gradle_scope"); it.entryAttributes.remove("test") }