First of all, thanks for adding documentation!

Secondly, you need to do a pass on all the docstrings here and fix:

   * The format is a bit funny, there is an extra indentation level that should not be there.
   * Now that Invenio will use sphinx style docstring, it would be good if we follow them (for consistency). This means basically instead of ```@param server: ...``` you use ```:param server:```

To take an example:

```
        """ Downloads a whole folder from the server.
            FtpDownloader.download_folder() will download all the files
            from the server in the working directory.

            @param folder: the absolute path for the folder on the server.

            @type folder: string
            @param target_folder: absolute or relative path for the
                                  destination folder default is the
                                  working directory.
            @type target_folder: string
            """
```

could be turned into:
```
        """ Downloads a whole folder from the server.

        FtpDownloader.download_folder() will download all the files
        from the server in the working directory.

        :param folder: the absolute path for the folder on the server.

        :type folder: string
        :param target_folder: absolute or relative path for the
                              destination folder default is the
                              working directory.
        :type target_folder: string
        """

```