Hello!
First of all, make sure you
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1. Using an application like phpmyadmin, export the tables (only the data and not the table creation part) from 1.6.0.: #__ebooks and #__ebooks_items (replace #__ with your Joomla database prefix).
You should have something like this (in my case the database prefix is jos_):
INSERT INTO `jos_ebooks` (`id`, `name`, `storage_place`, `description`, `cover_jpg`, `cover_html`, `copyright_page`, `credits_page`, `ack_page`, `introduction_page`, `introduction_section`, `index_page`, `version`, `opt_cover`, `opt_toc`, `opt_chapternumbering`, `opt_subchapternumbering`, `opt_usesection`, `opt_usecategory`, `opt_useitem`, `last_render`, `font_main`, `font_main_size`, `font_chapter`, `font_chapter_size`, `font_subchapter`, `font_subchapter_size`, `font_header`, `font_header_size`, `font_pageno`, `font_pageno_size`, `img_align`, `text_align`, `pageno_align`, `opt_ch_page`, `opt_subch_page`, `opt_heading`, `columns`, `opt_page_format`, `opt_left_margin`, `opt_right_margin`, `opt_top_margin`, `opt_bottom_margin`, `opt_unit`, `opt_chapter_font_color`, `opt_chapter_headline_bg_color`, `opt_main_font_color`, `opt_subchapter_font_color`, `opt_header_font_color`, `opt_pageno_font_color`, `opt_orientation`, `opt_custom_width`, `opt_custom_height`, `opt_mambot`, `opt_user_password`, `opt_admin_password`, `opt_lockpdf`, `opt_link_color`, `user_id`) VALUES
(1, 'Ebook 160', 'RjpcZWJvb2tzXzE2MFxhZG1pbmlzdHJhdG9yXGNvbXBvbmVudHNcY29tX2Vib29rc1xzdG9yYWdlXA==', 'Cras et metus non lectus venenatis dictum sed at magna. Quisque sodales, libero suscipit dictum sed.', NULL, '', '', '', '', '', NULL, '', '', 1, 1, 1, 1, 1, 1, 1, '2010-07-26 10:40:42', 'courier', 12, 'courier', 14, 'courier', 13, 'courier', '11', 'courier', '10', 'left', 'left', 'right', 1, 1, 'no', 1, 'a4', 11, 12, 13, 14, 'mm', '', '', '', '', '', '', 'P', '', '', 0, '', '', 0, '', 62);
INSERT INTO `jos_ebooks_items` (`id`, `bookid`, `sectionid`, `catid`, `itemid`, `itemorder`, `type`) VALUES
(1, 1, 1, 1, 1, 1, 'content'),
(2, 1, 1, 1, 6, 2, 'content'),
(3, 1, 1, 1, 9, 3, 'content'),
(4, 1, 1, 1, 44, 4, 'content'),
(5, 1, 1, 1, 45, 5, 'content');
2. Uninstall version 1.6.0.
3. Install version 1.6.3.
4. Using phpmyadmin again, import the content from step 1.
This way all your ebooks (only the settings and items and not the PDF's files; you'll have to render the ebooks again) will be transfered to 1.6.3.
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