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User should be able to fix unresolved references in Project properties dialog e.g. Broken reference would be displayed in list of compilation classpath elements, but in bold red font face with broken element icon and user would be able to fix it there by Fix button. The same would apply for any other kind of broken reference.
The spec in the URL field makes it easier to fix unresolved references, though not exactly the same way as Milan described.
Reevaluate.
I think this is a dupe.
Agreed with Jano and Hrebejk to do this after 4.1.
Tomas, moving java project specific issues to you for now.