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Java just isn't suited for this kind of problem. You can, as levent suggested, use JNI but you will find that in your case 90% of the code will be native and 10% will be Java. At that point it is easier to just use 100% native code.
One option you may want to look at is to create a Windows Explorer in Java. Then you can track what is going on in Java. I'm willing to bet that there is a Java File Explorer already out there if you Google for it.
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