Instead of Runtime.exec(String command) you need to use the signature of the exec(String command, String[] envp, File dir) method exec(String command, String[] envp, File dir) :
Process p = Runtime.getRuntime().exec("cmd /c upsert.bat", null, new File("C:\\Program Files\\salesforce.com\\Data Loader\\cliq_process\\upsert"));
But personally, I would use ProcessBuilder instead, which is a bit more verbose, but much easier to use and debug than Runtime.exec() .
ProcessBuilder pb = new ProcessBuilder("cmd", "/c", "upsert.bat"); File dir = new File("C:/Program Files/salesforce.com/Data Loader/cliq_process/upsert"); pb.directory(dir); Process p = pb.start();
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