Setting Java VM line.separator

Try using java -Dline.separator=$'\n'. That should do the trick, at least in bash.

Here is a test-run:

aioobe@r60:~/tmp$ cat Test.java 
public class Test {
    public static void main(String[] args) {
        System.out.println("\"" + System.getProperty("line.separator") + "\"");
    }
}
aioobe@r60:~/tmp$ javac Test.java && java -Dline.separator=$'\n' Test
"
"
aioobe@r60:~/tmp$ 

Note:

The expression $'' uses the Bash feature ANSI-C Quoting. It expands backslash-escaped characters, thus $'\n' produces a line feed (ASCII code 10) character, enclosed in single quotes. See Bash manual, section 3.1.2.4 ANSI-C Quoting.