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While setting up freeform projects in 4.1rc1 and adding new classpaths to the project via "Properties|Java Sources Classpath" there is no way to specify a relative class path. In addition, if the project.xml is manually edited to use a relative path which is _outside_ the project, those paths are converted to absolute paths upon modification of path structure. While not critical to compiliation, it breaks code completion, etc..
Paths will be made relative automatically if you register a VCS working directory in Versioning Manager. However there should still be a UI to override this guess. Cf. issue #49637 for j2seproject.
Probably would not happen the same way in 5.0. There are other issues filed for the more general management of external paths.