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The 3.5.0 migration notes should describe how clean start is now performed as the nano changes will impact anyone who has written their own script or other means of clean starting Virgo (e.g. perhaps Frieder's Maven plugin). See http://wiki.eclipse.org/Virgo/Community/Migrating_from_3.0.x_to_3.5.0
After solving bug 367830 that enables clustering this bug is no longer valid. That is because -clean now behaves exactly like it always did: delete serviceability and work.