public void startProgram() {
    try {
        deleteWDB(configuration.getPath() + File.separator + "WDB");
        // runtime and other stuff
    } catch (IOException e) {
        // stuff
    }
}

public void deleteWDB(String path) {
    File file = new File(path)
    if (file.isDirectory())
        File files[] = file.getFiles() // might be something like listFiles or something with list
        foreach File f in files
            deleteWDB(f.getAbsolutePath()); // should be a function that at least semantically is called this
    } else if (file.exists()) { // or some variation of file validation to make sure its an actual file
        System.out.println(file.getAbsolutePath()); // just for debug, keep this in and next line uncommented until fully bugtested to make sure you dont delete accidental files
        file.delete()
    }
}