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This bug is to backport this fix to 3.3.2 P +++ This bug was initially created as a clone of Bug #372683 +++ As can be shown by bug 363863 , configurations which have been supported by WTP up until now - the allowance of the creation of various projects with the default source folder being mapped to the default output folder - will be marked as an error by JDT validation. To more fully support the JDT and its changes, we need to remove our automated support for merging the source and output folders for EJBs (and thus EJB Clients), JCAs, AppClients, and Utility projects. This impacts org.eclipse.jst.j2ee/j2eeplugin/org/eclipse/jst/j2ee/internal/plugin/JavaeePreferencesInitializer
Created attachment 212307 [details] The same fix as 3.4.0
Sorry this was laying around for so long... approved