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When developing plug-ins, two mistakes arise from the fact that the user can manually change the java build path: runtime errors (NoClassDefFound exceptions) and compile errors when exporting. I suggest that PDE listens to the java model, and more precisely to the flags: F_CLASSPATH_CHANGED, F_ADDED_TO_CLASSPATH, F_CLASSPATH_REORDER. CC'ing Jerome who gave me the info about the flags
Another way to prevent the user from messing with the build path (when inside a PDE project) would be to remove the Java Build Path wizard and the 'Build Path' context menu.
The rational is: when using a PDE project, only the plugin.xml should be used to change the build path
best addressed as part of the bigger build.properties validation item. *** This bug has been marked as a duplicate of 34165 ***