src/Tools/Setup/isabelle/setup/Build.java

             InputStream in_orig = System.in;
             PrintStream out_orig = System.out;
             PrintStream err_orig = System.err;
             ByteArrayInputStream in = new ByteArrayInputStream(new byte[0]);
             ByteArrayOutputStream out = new ByteArrayOutputStream();
-            PrintStream out_stream = new PrintStream(out);
 
             // Single-threaded context!
             try {
+                PrintStream out_stream = new PrintStream(out);
                 System.setIn(in);
                 System.setOut(out_stream);
                 System.setErr(out_stream);
                 ok = new MainClass().process(args.toArray(String[]::new));
+                out_stream.flush();
             }
             finally {
                 System.setIn(in_orig);
                 System.setOut(out_orig);
                 System.setErr(err_orig);