If you use the readLine and println methods, Java automatically deals with the platform differences for you.
The last line in a file may or may not have a line separator.
I am not sure what the best technique for writing Unix-convention \n files on Windows is. You could try setting the line.separator system property, though Oracle recommends against it.
// prepare to produce Unix-format text files on a Windows machine System.setProperty( "line.separator", "\n" );
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