I am using java.util.zip to add some configuration resources into a jar file. when I call addFileToZip() method it overwrites the jar completely, instead of adding the file to the jar. Why I need to write the config to the jar is completely irrelevant. and I do not wish to use any external API's.
EDIT: The jar is not running in the VM and org.cfg.resource is the package I'm trying to save the file to, the file is a standard text document and the jar being edited contains the proper information before this method is used.
My code:
public void addFileToZip(File fileToAdd, File zipFile)
{
    ZipOutputStream zos = null;
    FileInputStream fis = null;
    ZipEntry ze = null;
    byte[] buffer = null;
    int len;
    try {
        zos = new ZipOutputStream(new FileOutputStream(zipFile));
    } catch (FileNotFoundException e) {
    }
    ze = new ZipEntry("org" + File.separator + "cfg" + 
            File.separator + "resource" + File.separator + fileToAdd.getName());
    try {
        zos.putNextEntry(ze);
        fis = new FileInputStream(fileToAdd);
        buffer = new byte[(int) fileToAdd.length()];
        while((len = fis.read(buffer)) > 0)
        {
            zos.write(buffer, 0, len);
        }           
    } catch (IOException e) {
    }
    try {
        zos.flush();
        zos.close();
        fis.close();
    } catch (IOException e) {
    }
}