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Originally Posted by Diruuo
Question #1: Do I need to remove all of these manually copied books from my device so that Calibre can send updated versions of them?
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Calibre has no problem with the source of the books. If it can match the books on the device to one in its library, it will work. If there is a problem with the version of the book on the device, you might have to remove the book and resend it. The Kobo devices process them the first time the book is seen. During this, it extracts the metadata including the ToC. These are stored in the internal database. If you resend the book using calibre, changes to the metadata and ToC are not picked up. If you change the ToC, or internal structure of the book, you need to remove it before resending. But, if it is just metadata changes, you can use my Kobo Utilities plugin to update the database on the device instead.
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When I say I had "shelves working" I meant "I did all of the steps in the Sticky thread, and nothing exploded" working. I have no idea how to employ those shelves for management of my books.
Question #2: If I have setup Calibre as shown in the Sticky, have a plugboard setup (as per the Sticky again) how do I then use those things to my advantage by making (or populating) the actual Shelves so that I can send them to my device?
Question #3: How do I send Shelves to my device or does the device simply organize things in Shelves based on metadata?
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Collections, or shelves as Kobo used to call them, are a way of grouping books together on the device. What the groups are, is completely up to you. How you use them, is up to you. Some people like a collection for each series. Or based on some sort of tag.
If you do the collection management from calibre, it is based on metadata in the library. You choose one or more columns and when the device is connected, calibre will create the collections and add or remove books from them as needed.
The plugboards have nothing to do with the collections. They are a way to fiddle with the metadata as the book is sent to the device. The reason to do this is because the different devices don't handle the metadata as well as calibre does. And the most common reason is that none of the devices handle the series info well. The Kobo devices show the series, but they don't allow sorting on the series info. So, a lot of people use a the plugboard to prefix the book title with the series info so that a title sort will work.
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I think I value the ability for quicker page turning more then I care about the space taken up by the Header and Footer when it comes to Kepub vs epub. I'm not sure if there are any other major differences that I care about.
Question #4: If I decide that I want to read only in Kepub instead of epub, how do I make it so that Calibre automatically converts when sending to the device?
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If you want to use kepubs, you need use either the KoboTouchExtended driver or the Kepub Output plugin. The former converts the books to kepub as they are sent to the device and the latter allows you to convert the books to kepub in the calibre library and send using the standard KoboTouch driver. Either of these can be installed from the plugin section of the calibre preferences.