I store my source file like this:
+-java -> for java source
+-test -> for junit test.
I add both java and test as source directory and when i use default configuration, that is "$CLASS$", "test/$CLASS$Test", it works. and whne i changed to "src/java/$DIRECTORY$/$CLASS$" and "src/test/$DIRECTORY$/$CLASS$", junit plugin breaks when i create a new unit test by saying "...string index out of index -1...". and what's worse is even i change back the setting, i still got the error.