下面是我的代码，它打算获取两个.ckl文件，比较两个文件，添加新项目并创建一个新的合并文件。该程序在Netbeans中运行时可以正确执行，但是，当执行.jar时，该程序似乎未使用UTF-8编码文件。我对编程很陌生，想知道在什么地方或如何执行这种编码？

**我删除了Swing代码和其他行，以便仅显示我的方法，该方法完成所有比较和合并。

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();
    }

}