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Using Chroot with a Java application

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http://askubuntu.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 Ubuntu. 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've looked at the community documentation for using chroot, but it says to set up a basic installation of Ubuntu in it. Is this really necessary? All I want is to run Java applications inside it so the app thinks it is in its own fake filesy (HowTos)