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The jar file is needed in the class path of your java project. If you're using an IDE, your project probably has a lib or libs folder where it would fit. Alternatively, your IDE probably has an "add library" menu entry somewhere, when you right click your project.
The .so file, along with the others, needs to be loaded at runtime. The standard path for that is something like /usr/lib and friends, where the system looks for dynamic libraries by default. Alternatively (and it would probably be cleaner), you can tell your IDE to run your application with the -Djava.library.path=/home/you/whereveryouhavethesofiles option passed to the Java VM.
Hope that helps...
