Ok, I was wrong, the binaries are not right. In your classpath you need jinput.jar and jutils.jar then in the directory you run from you need a controller directory that contains libjinput.so and linux.jar
The test I did was to create a new empty directory, I copied the jinput.jar and jutils.jar to that directory, I created a controller directory and copied libjinput.so and linux.jar to the controller directory so I ended up with
and then ran
java -cp jinput.jar:jutils.jar net.java.games.input.test.ControllerTextTest
it found the linux plugin fine.
You can move jinput.jar and jutils.jar around as long as you update your classpath. If you move the plugin then you must use the plugin property to cope.
For example, with a fresh copy of the binary the following command works
java -cp coreAPI/bin/jinput.jar:\
Note that the library path needs to be updated so that the .so can be loaded.