Running a Java application in its own fake filesystem

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http://stackoverflow.com – I'm working on designing a group of Java programs that I hope to turn into a Java-based OS someday. Until I get a kernel working, I want to just run them on top of a Linux system (I'm using Ubuntu, if that matters). Because of this, I need all filesystem calls directed to a different directory in my home folder, so accessing / from within Java would actually access /home/<user>/Thunderbolt/. I basicly need the same thing as in this question, and also this question, but for Java. I've seen stuff about chroot, and I think this might work, but I have no idea how to get it to work with Jav (HowTos)