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Moved from bug 40720. Project->properties->Java Build Path-> Add Library -> JRE System Library -> Alternative Library -> Finish. The Alt lib is added to the libraries tab but the OK button is not highlighted bc I have a variable JRE_LIB=x/rt.jar which also contained that rt.jar. The error message is displayed in the header of the tab, this is not obvious and even after repeating the process 5 times I didn't notice the error message until it was pointed out. Perhaps changing the background color of the message to a light red would highlight it or moving the error message to a popup dialog would work better.
The animated message status function provided in Eclipse 3.2 resolves this issue. See Bug 129829 *** This bug has been marked as a duplicate of 129829 ***