NPM uses a lot of symbolic links. When Trireme creates them, it tries to make them into absolute paths relative to the current working directory, which is wrong for two reasons. First of all, it comes up with the wrong answer, and second of all, it means that the link doesn't get created in a relative way so that you can't move it around with the rest of the directory.
Note that this fix will only work for Java 7 since Java 6 does not support symbolic links.
Fixed in 0.7.1.