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In bug259981 we changed the behavior of the cleanupOnOpen option to also cleanup on any save operation. We probably should have a cleanupOnSave option instead of reusing the cleanupOnOpen option.
Fixed in master with commit: http://git.eclipse.org/c/equinox/rt.equinox.framework.git/commit/?id=95348af9861e192c7efdf8334fb57458470345f2