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How can this be improved?

/*
 * To change this template, choose Tools | Templates
 * and open the template in the editor.
 */
package pdf_merging_70112016;

import com.lowagie.text.Document;
import com.lowagie.text.DocumentException;
import com.lowagie.text.pdf.PdfContentByte;
import com.lowagie.text.pdf.PdfImportedPage;
import com.lowagie.text.pdf.PdfReader;
import com.lowagie.text.pdf.PdfWriter;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.util.ArrayList;
import java.util.List;
import properties.ApplicationProperties;

/**
 *
 * @author
 */
public class PDFMerging {

    public void mergePDF() throws FileNotFoundException {
        ApplicationProperties prop = ApplicationProperties.getInstance();
        prop.loadProperties();
        String temppath = prop.getClickProperty("tempPath");
        String FAQPath = prop.getClickProperty("FAQPath");
        String finalPDFParh = prop.getClickProperty("finalPath");
        String errorPath = prop.getClickProperty("errorPath");
        String outputFilename = "";


        File tempFolder = new File(temppath);
        File FAQFolder = new File(FAQPath);
        File[] listOfTempFiles = tempFolder.listFiles();
        File[] listOfFAQFiles = FAQFolder.listFiles();

        for (int i = 0; i < listOfTempFiles.length; i++) {
            for (int j = 0; j < listOfFAQFiles.length; j++) {
                if (listOfTempFiles[i].isFile() && listOfTempFiles[i].length() > 0) {
                    if (listOfTempFiles[i].getName().toLowerCase().contains(".pdf")) {
                        if (listOfTempFiles[i].getName().substring(listOfTempFiles[i].getName().lastIndexOf("#") + 1).equals(listOfFAQFiles[j].getName())) {
                            try {
                                List<InputStream> list = new ArrayList<InputStream>();
                                list.add(new FileInputStream(listOfTempFiles[i]));
                                list.add(new FileInputStream(listOfFAQFiles[j]));
                                System.out.println(listOfTempFiles[i].getName() + "with FAQ: " + listOfFAQFiles[j].getName());
                                int iend = listOfTempFiles[i].getName().lastIndexOf("#");
                                if (iend != -1) {
                                    outputFilename = listOfTempFiles[i].getName().substring(0, iend);
                                }
                                OutputStream out = new FileOutputStream(new File(finalPDFParh + "/" + outputFilename + ".pdf"));
                                doMerge(list, out);
                                list.clear();
                            } catch (FileNotFoundException e) {
                                e.printStackTrace();
                            } catch (DocumentException e) {
                                e.printStackTrace();
                            } catch (IOException e) {
                                e.printStackTrace();
                            }
                        }
                        if (listOfTempFiles[i].getName().substring(listOfTempFiles[i].getName().lastIndexOf("#") + 1).toUpperCase().contains("NA")) {
                            int iend = listOfTempFiles[i].getName().lastIndexOf("#");
                            if (iend != -1) {
                                outputFilename = listOfTempFiles[i].getName().substring(0, iend);
                            }
                            listOfTempFiles[i].renameTo(new File(finalPDFParh + "/" + outputFilename + ".pdf"));


                        }






                    }
                } else {
                    listOfTempFiles[i].renameTo(new File(errorPath + "/" + outputFilename + ".pdf"));
                }

            }
        }

    }

    public static void doMerge(List<InputStream> list, OutputStream outputStream)
            throws DocumentException, IOException {
        Document document = new Document();
        PdfWriter writer = PdfWriter.getInstance(document, outputStream);
        document.open();
        PdfContentByte cb = writer.getDirectContent();

        for (InputStream in : list) {
            PdfReader reader = new PdfReader(in);
            for (int i = 1; i <= reader.getNumberOfPages(); i++) {
                document.newPage();
                //import the page from source pdf
                PdfImportedPage page = writer.getImportedPage(reader, i);
                //add the page to the destination pdf
                cb.addTemplate(page, 0, 0);
            }
        }

        outputStream.flush();
        document.close();
        outputStream.close();
    }
}
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  • Remove the automatically generated comment at the top of the file.
  • Instead of using printStackTrace, either throw the exception or log the (expected) exception and continue.
  • Any file you open must be closed again. Use try-with-resources for that.
  • list.clear() is unnecessary. Just let the garbage collector do its work.
  • Use for (File faqFile : faqFiles) instead of counting j.
  • Since listOfFAQFiles is not a list but an array, don't call it list. Just faqFiles is simpler and enough.
  • Instead of passing open streams around, prefer to pass the files. This makes it easier to close the streams, even when an exception occurs.
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