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I've had Eclipse run out of memory a few times when working with a large project. After I clicked ok on the error dialog, it then proceeded to try to save metadata, but because it was out of memory, this resulted in corruption. As a result, the only work around was to reinstall Eclipse, any plugins, and rebuild all the projects, saving any changed worked. I would suggest that the Eclipse error handling for exiting when out of memory ensure that it does NOT save the workspace & metadata, to avoid this kind of error. This may also affect JDT.
*** This bug has been marked as a duplicate of 3128 ***