export/zip eclipse project via java program for Windows and MAC

I need to export a (java) eclipse project without using eclipse. I tried to copy all relevant files and pack them with a ZipOutputStream. So good so far, I can load this zip-file in Windows. But MAC users have the problem, that the file structure is not automaticaly detected and create files with names like "vorlage\src\de\tuberlin..." next to the src directory. (example picture)

Is there a way to properly export an eclipse project with a java programm?

The reason is that I created programming exercises for a lecture and marked the solutions with special comments. During copying the files these comments and the solutions are left out.

One solution would be importing the zip-file in Windos and exporting again with the help of eclipse. But this costs a lot of time doing this for each exercise.

Although I cannot see any difference between the two zip-files, there seems to be something.

Here my code to copy the files:

public static void copyDir(File source, File target, ArrayList<String> exclude)
throws FileNotFoundException, IOException {

    File[] files = source.listFiles();
    File newFile = null;
    target.mkdirs();
    if (files != null) {
        for (int i = 0; i < files.length; i++) {
            newFile = new File(target.getAbsolutePath() + System.getProperty("file.separator") + files[i].getName());
            if (files[i].isDirectory()) {
                copyDir(files[i], newFile, exclude);
            }
            else if ( !exclude.contains(files[i].getName()) ) {
                copyFile(files[i], newFile);
            }
        }
    }
}

public static void copyFile(File file, File target) throws FileNotFoundException, IOException {

    if (file.getName().endsWith(".java")) {
        copyJavaFile(file, target);
        return;
    }

    BufferedInputStream in = new BufferedInputStream(new FileInputStream(file));
    BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(target, true));
    int bytes = 0;
    while ((bytes = in.read()) != -1) {
        out.write(bytes);
    }
    in.close();
    out.close();
}


private static void copyJavaFile(File file, File target) throws IOException {

    BufferedReader in = new BufferedReader(new FileReader(file));
    PrintWriter out = new PrintWriter(target);
    boolean stopped = false;
    String line = null;
    while ( (line = in.readLine() ) != null) {
        stopped |= line.contains("IF EXCLUDE");
        if (!stopped && !line.contains("ENDIF"))
            out.println(line);
        stopped &= !line.contains("ELSE");
    }
    in.close();
    out.close();
}

I copy the following (sub-)directories/files:

• .settings


• src


• .classpath


• .project

I create the zip-file with:

public Zip(final File projDir, final File outFile) {
    ZipOutputStream output = null;
    try {
        output = new ZipOutputStream(
                    new BufferedOutputStream(
                        new FileOutputStream(outFile)));
        for (File file : projDir.listFiles()) {
            writeFiles(file, output, "");
        }
        output.finish();
    } catch (IOException ex) {
        System.err.println("IO Error: " + ex.getMessage());
    } finally {
        try {output.close();} catch (IOException ex) {}
    }
}

private void writeFiles(File f, ZipOutputStream output, String dir) throws IOException {
    if (f.isDirectory()) {
        // recursively write files in directory
        for (File file : f.listFiles()) {
            writeFiles(file, output, dir + f.getName() + File.separator);
        }
    } else {
        // write this file to archive
        FileInputStream fis = new FileInputStream(f);
        ZipEntry entry = new ZipEntry(dir + f.getName());
        entry.setTime(f.lastModified());
        output.putNextEntry(entry);
        copy(fis, output);
        output.closeEntry();
        fis.close();
    }
}

private void copy(InputStream is, OutputStream os) throws IOException {
    byte[] buffer = new byte[1024];
    int bytes;
    while ((bytes = is.read(buffer)) > 0) {
        os.write(buffer, 0, bytes);
    }
}