Diese Frage hat hier bereits eine Antwort:

Below ist mein Code, es ist vorgesehen, zwei .ckl-Dateien zu nehmen, die beiden zu vergleichen, die neuen Elemente hinzuzufügen und eine neue zusammengeführte Datei zu erstellen. Das Programm wird korrekt ausgeführt, wenn es in Netbeans ausgeführt wird. Beim Ausführen der JAR-Datei scheint das Programm die Datei jedoch nicht in UTF-8 zu codieren. Ich bin ziemlich neu in der Programmierung und möchte wissen, wo oder wie ich diese Codierung erzwingen muss, um stattfinden zu können?

** Ich habe den Swing-Code und andere Zeilen entfernt, sodass nur meine Methode angezeigt wird, die Methode, die das Vergleichen und Zusammenführen übernimmt.

public void mergeFiles(File[] files, File mergedFile) {

    ArrayList<String> list = new ArrayList<String>();

    FileWriter fstream = null;
    BufferedWriter out = null;
    try {
        fstream = new FileWriter(mergedFile, false);
        out = new BufferedWriter(fstream);
      } catch (IOException e1) {
        e1.printStackTrace();
    }
    // Going in a different direction. We are using a couple booleans to tell us when we want to copy or not. So at the beginning since we start
    // with our source file we set copy to true, we want to copy everything and insert vuln names into our list as we go. After that first file 
    // we set the boolean to false so that we dont start copying anything from the second file until it is a vuln. We set to true when we see vuln
    // and set it to false if we already have that in our list. 
    // We have a tmpCopy to store away the value of copy when we see a vuln, and reset it to that value when we see an </VULN>
    Boolean copy = true;
    Boolean tmpCopy = true;
    for (File f : files) {
        textArea1.append("merging files into: " + mergedFilePathway + "\n");
        FileInputStream fis;
        try {
            fis = new FileInputStream(f);
//                BufferedReader in = new BufferedReader(new InputStreamReader(new FileInputStream(mergedFile), "UTF-8"));
            BufferedReader in = new BufferedReader(new InputStreamReader(fis));
            String aLine;
            while ((aLine = in.readLine()) != null) {
                // Skip the close checklist and we can write it in at the end
                if (aLine.trim().equals("</iSTIG>")) {
                    continue;
                }
                if (aLine.trim().equals("</STIGS>")) {
                    continue;
                }
                if (aLine.trim().equals("</CHECKLIST>")) {
                    continue;
                }
                if (aLine.trim().equals("<VULN>")) {
                    // Store our current value of copy
                    tmpCopy = copy;
                    copy = true;
                    String aLine2 = in.readLine();
                    String aLine3 = in.readLine();
                    String nameLine = in.readLine();

                    if (list.contains(nameLine.trim())) {
                        textArea1.append("Skipping: " + nameLine + "\n");
                        copy = false;
                        while (!(aLine.trim().equals("</VULN>"))) {
                            aLine = in.readLine();
                        }
                        continue; // this would skip the writing out to file part
                    } else {
                        list.add(nameLine.trim());
                        textArea1.append("::: List is now :::");
                        textArea1.append(list.toString() + "\n");
                    }
                    if (copy) {
                        out.write(aLine);
                        out.newLine();
                        out.write(aLine2);
                        out.newLine();
                        out.write(aLine3);
                        out.newLine();
                        out.write(nameLine);
                        out.newLine();
                    }
                } else if (copy) {
                    out.write(aLine);
                    out.newLine();
                }
                // after we have written to file, if the line was a close vuln, switch copy back to original value
                if (aLine.trim().equals("</VULN>")) {
                    copy = tmpCopy;
                }
            }

            in.close();
        } catch (IOException e) {
            e.printStackTrace();
        }
        copy = false;
    }

    // Now lets add the close checklist tag we omitted before
    try {
        out.write("</iSTIG>");
        out.write("</STIGS>");
        out.write("</CHECKLIST>");
    } catch (IOException e) {
        e.printStackTrace();
    }

    try {
        out.close();
    } catch (IOException e) {
        e.printStackTrace();
    }

}