There's a fundamental problem with your goal, in that Java is a scripting language, which needs a CLR to run, which depends on an OS. So you cannot build an OS on top of a scripting language sitting on a CLR on top of an OS (or you could, but what would be the point).

More to the point, you could just take an existing environment and remove all file associations other than .js, so that it would only handle Java (something along those lines). Use one of the limited OS environments, that has most stuff already stripped out, like Windows Mobile or Android.

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