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Certain preferences, such as many of the Java ones, do not make sense to be a per-workspace preference, as my coding style or JavaDoc templates are generally not going to change from workspace to workspace. It would be nice if a mechanism to allow preferences to be marked as "global" (i.e. not per-workspace) existed, rather than relying on exporting from one workspace and importing them into another.
This bug is the same as a plan item for the 3.0 development cycle.... *** This bug has been marked as a duplicate of 36965 ***