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This one works... using && operator you can add one or commands to be executed in same command prompt

try {
    Process p = Runtime
                    .getRuntime()
                    .exec("cmd /c start cmd.exe /K \"dir && ping localhost && echo end\"");
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } 

Consider the solution in here also

Update from the questioner: Solution to execute commands in cygwin

getRuntime().exec("cmd /c start C:/cygwin64/bin/bash.exe --login -c \"ls ; whoami ; exec bash\"");