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Biggest changes required here involved the new VirtualFile interface as we needed to convert them to java.io.File in a number of places. I tried to keep the conversions to a minimum, so that we don't bump into unexpected things such as issues with `jrt` filesystem and tried using Path wherever possible. I am not 100% if everything is correct, but I double checked and everything seems in place. We also needed to adjust ScalaInstance to make it work with the new interface and add an additional setting for output in the Java compilers, since otherwise everything gets produced to source directories (this mirrors the change in zinc itself.)
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