demo, Java - rextester

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//'main' method must be in a class 'Rextester'.
//Compiler version 1.8.0_111

import java.util.*;
import java.lang.*;

class Rextester {
    public static void main(String args[]) {
        String input = "1,2,3..6..8,9..11";
        String[] parts = input.split(",");
        List<Integer> list = new ArrayList<>();

for (String part : parts) {
            if (!part.contains("..")) {
                list.add(Integer.parseInt(part));
            }
            else {
                String[] ranges = part.split("\\.\\.");
                for (int i=0; i < ranges.length-1; ++i) {
                    int start = Integer.parseInt(ranges[i]) + (i == 0 ? 0 : 1);
                    int end = Integer.parseInt(ranges[i+1]);
                    for (int j=start; j <= end; ++j) list.add(j);
                }
            }
        }

// print list of numbers
        for (int i=0; i < list.size(); ++i) {
            System.out.print((i > 0 ? ", " : "") + list.get(i));
        }
    }
}

[ + ] Show input
Compilation time: 0.62 sec, absolute running time: 0.14 sec, cpu time: 0.07 sec, memory peak: 18 Mb, absolute service time: 0,77 sec