this is old. It uses github.com/javaparser/javaparser . Problem was javadocs added and twice. You are using INRIA/spoon library right now

CommentGenerator.java

package com.nerzid.autocomment.generator;

import com.github.javaparser.ASTHelper;
import com.github.javaparser.JavaParser;
import com.github.javaparser.ParseException;
import com.github.javaparser.ast.CompilationUnit;
import com.github.javaparser.ast.body.MethodDeclaration;
import com.github.javaparser.ast.body.Parameter;
import com.github.javaparser.ast.body.TypeDeclaration;
import com.github.javaparser.ast.comments.JavadocComment;
import com.github.javaparser.ast.visitor.VoidVisitorAdapter;
import com.nerzid.autocomment.errorhandler.Errors;
import com.nerzid.autocomment.filehandler.FilePicker;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.nio.file.Files;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.logging.Level;
import java.util.logging.Logger;
import java.nio.charset.StandardCharsets;


/**
 *
 * @author nerzid
 */
public class CommentGenerator {

    public static ArrayList<File> files_list;

    public static void main(String[] args) throws FileNotFoundException, IOException {
        files_list = FilePicker.chooseAndGetJavaFiles();
        
        if (files_list == null || files_list.isEmpty()) {
            Errors.showError(Errors.COMMENT_GENERATOR_FILELIST_NULL_OR_EMPTY);
        } else {

            CompilationUnit cu = null;

            files_list.get(0).setWritable(true);
            FileInputStream in = new FileInputStream(files_list.get(0));
            try {
                //cu = JavaParser.parse(in);
                cu = JavaParser.parse(files_list.get(0), StandardCharsets.UTF_8);

            } catch (ParseException ex) {
                Logger.getLogger(CommentGenerator.class.getName()).log(Level.SEVERE, null, ex);
            } finally {
                in.close();
            }
            new MethodChangerVisitor().visit(cu, null);
            TypeDeclaration asd;

            System.out.println(cu.toString());
            File modified = files_list.get(0);

            Files.write(files_list.get(0).toPath(), Arrays.asList(cu.toString()), StandardCharsets.UTF_8);
        }
    }

    private static class MethodChangerVisitor extends VoidVisitorAdapter {

        @Override
        public void visit(MethodDeclaration n, Object arg) {
            // change the name of the method to upper case
            if (n.getName().equals("deneme")) {
                n.setName(n.getName().toUpperCase());
            } else {
//                JavadocComment doc = n.getJavaDoc();
//                doc = new JavadocComment("nice comment there");
//
//                System.out.println("doccc: " + doc);
//                n.setName("changedMethodName");
//                n.setJavaDocComment(doc.toString());
//                n.setJavaDocComment("Pls ol");
//                n.setBlockComment("asdad");
                //n.setLineComment("asdadad");
                System.out.println("Javadoc: " +n.getJavaDoc().toString());
            }

            System.out.println("javadoc: " + n.getJavaDoc());

            // create the new parameter
            Parameter newArg = ASTHelper.createParameter(ASTHelper.INT_TYPE, "value");
            // add the parameter to the method
            n.addParameter(newArg);

        }
    }

}