I have the an build.xml that allows me to run junit tests. Here is the relevant part:
You can always symlink your jar to another location if you are on linux. This way you could symlink it to a path that does not include the version. For example:
ln -s plugins/org.junit4_4.5.0.v20090824/junit.jar /wherever/junit.jar
You may want to have a libraries folder outside of the eclipse subdirectories. You could also consider using ivy or maven to manage your dependencies.
I'm not sure why your above example fails, but the error message implies that junit.jar is not found. Are you sure that eclipse.home is set? You could echo it with: