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The next update (I'm not sure when exactly) is going to have a few changes to the options. So, please take note of what options you have selected as you will most likely find that you'll need to update your selected options!
First, the three database trigger options (the last three options) are going away, in favour of being moved into the Kobo Utilities plugin. It's unlikely that this update will coincide with an update to Kobo Utilities adding those options, but as far as I'm aware they're being added and based on how Kobo Utilities adds triggers I expect it to be better than how I was handling it.
Second, the option to delete files not in the manifest is going away. When I had my own OEB Container implementation, it was fairly trivial to do this at the same time as I was processing files in the ePub. Now with calibre's standard implementation being used, it's not so easy to do and it seems to me that it's more work than it's really worth considering it's really for technical accuracy and didn't give a noticeable improvement in most cases.
Third, the location of the reference KePub file is changing. Right now, the directions tell you to find calibre's configuration directory, go to the 'plugins' folder, and put reference.kepub.epub in the 'KoboTouchExtended' directory. With the next update, 'KoboTouchExtended' won't be used and reference.kepub.epub should be put directly in the 'plugins' folder.
As part of this, for those of you who have been asking for a way to generate KePub files without having a Kobo device attached, I'm working on an output format plugin for calibre's conversion process.
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