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The project properties does not have any means of adding an external folder to the current project. I do not remember seeing this issue in 4.0 Beta1. I tried with both my J2SE and J2ME projects and have the same issue.
If you are talking about the classpath then you surely can add a folder in the project properties -> compiling sources -> Add Jar folder. But I think you are asking for a project with more source roots. *** This issue has been marked as a duplicate of 46354 ***
This issue was solved long time ago. Because nobody has reopened it neither added comments, we are verifying/closing it now. If you are still able to reproduce the problem, please reopen. Thanks in advance.