Edits txt file when it should not

/*********************************************************************************
 * (Add package statement) Suppose you have Java source files under the           *
 * directories chapter1, chapter2, . . . , chapter34. Write a program to insert   *
 * the statement package chapteri; as the first line for each Java source file    *
 * under the directory chapteri. Suppose chapter1, chapter2, . . . , chapter34    *
 * are under the root directory srcRootDirectory. The root directory and chapteri *
 * directory may contain other folders and files. Use the following command to    *
 * run the program:                                                               *
 *                                                                                *
 * java Exercise_12_18 srcRootDirectory                                           *
 *                                                                                *
 *********************************************************************************/
import java.util.*;
import java.io.*;

public class _12_18_Alt {
    /** Main method */
    public static void main(String[] args) throws Exception {
        // Check command line parameter usage
        if (args.length != 1) {
            System.out.println("Usage java Exercise_12_18 srcRootDirectory");
            System.exit(1);
        }

        // Check if file object is a Directory
        File rootDir = new File(args[0]);
        if (!rootDir.isDirectory()) {
            System.out.println("Directory " + args[0] + " does not exist");
            System.exit(2);
        }

        // Create list of directories
        ArrayList<File> chapters = getDirectories(rootDir);

          //PRINT ENTIRE CONTENTS OF DIRECTORY
        for (int i = 0; i <chapters.size() ; i++) { //Array of all chapter files
            System.out.println(chapters.get(i));
        }

        while (!chapters.isEmpty()) {
            // Create array of chapter files
            ArrayList<File> files = getFiles(chapters);

            insertStatement(files, chapters.get(0));

            chapters.remove(0);

            System.out.println("***Print contents of files array below***");
            for (int i = 0; i <files.size(); i++) {
                System.out.println(files.get(i));
            }
        }

    }

    /** Adds all Java source files in directory to list */
    public static ArrayList<File> getFiles(ArrayList<File> dir) {
        if (!dir.get(0).isDirectory()) {
            System.exit(0);
        }
        ArrayList<File> list =
                new ArrayList<>(Arrays.asList(dir.get(0).listFiles()));


        filterJavaFiles(list);
        return list;
    }

    /** Inserts a string as first line for each file in a list */
    public static void insertStatement(ArrayList<File> list, File dir)
            throws Exception {
        for (int i = 0; i < list.size(); i++) {
            ArrayList<String> lines = new ArrayList<>();
            lines.add("package " + dir.getName() + ";");

            try (
                    // Create input file
                    Scanner input = new Scanner(list.get(i));
            ) {
                while (input.hasNext()) {
                    lines.add(input.nextLine());
                }
            }

            try (
                    // Create input file
                    PrintWriter output = new PrintWriter(list.get(i));
            ) {
                for (int j = 0; j < lines.size(); j++) {
                    output.println(lines.get(j));
                }
            }
        }
    }

    /** Removes non-Java source files from list */
    public static void filterJavaFiles(ArrayList<File> list) {
        for (int i = 0; i < list.size(); i++) {
            String str = list.get(i).getName();
            boolean isjavaCode = str.substring(str.lastIndexOf('.')).equals(".java");
            System.out.println("BOOLEAN TEST: " + i + str.substring(str.lastIndexOf('.')));
            if (!isjavaCode)
                list.remove(i);
        }
    }

    /** Generates File objects and adds them to list */
    public static ArrayList<File> getDirectories(File root) {
        ArrayList<File> directories = new ArrayList<>();
        for (int i = 1; i < 34; i++) {
            directories.add(new File(root, "chapter" + i));
        }
        return directories;
    }
}