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In some use cases it's preferable to have for example the nanorc configs inside a jar. Although a lot of the code base use `java.nio.file.Path`, a couple of places still call `Path.toFile()`, which isn't supported for NIO's ZIP file system, which can be created for a `jar:` URL, so that the contents of the jar can be used as a (read only) file system. This PR replaces occurences of `Path.toFile()` and replaces the `File` operations with NIO's `Files`.
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