+2  A: 

Your question isn't completely clear, but I will give a general answer...

In Java there is only two ways to get Java to look in a .jar file (and they really boil down to one way in the end), and that's to specify the .jar file in the classpath, or to create a classloader that will look in that jar file and add it to the list of classloaders Java will use.

And, of course, all the classpath is is a set of classloaders that Java instantiates and uses before your program even starts.

So a JNI program needs to make the Java calls (which I'm not looking up just now) to set up a new class loader and get Java to start using it if the JNI program needs Java to start looking in additional .jar files.

Omnifarious