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Originally Posted by skn
So, would the right answer be that set management to automatic
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Yes.
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and add series, series_index and timestamp to template (see image)?
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That is completely up to you. This template is used to set the filename on the device. Kobo devices don't really use it. The books need a unique name, but, the device tries to get the title, author and some other metadata from the metadata contained in the book, not from the filename. It will use the filename for the title if it cannot do this.
Personally, the only change I have made to the default is to add the name of the library in the path to reduce the number of directories in the root of the device. That was only done for convenience because I do look at the device when testing things.
Also, the save template on the "Sending books to devices" page is a default used by the drivers. If you change the driver configuration, the save template is copied to the device configuration and will need to be changed there in the future.
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Should there also be #collections included in template or is it controlled elsewhere? Collections have worked fine so far (but I am not sure if I nulled setting now...).
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The collections are controlled by the driver. You configure this in the driver configuration. The series info is also done by the driver and again, it has the configuration for whether to update the series info and other metadata.
With the metadata management set to automatic, when you connect the device, the driver will update the metadata on the device for all the books on the device that are in the library. For Kobo devices, the driver can update the database on the device directly. This is what the device gets the metadata and collections while you are using it. The driver will update the device with any changes in the library since the last time it was connected. This is needed for the series info as the device does not read it from the books. There are some other metadata that this happens with, but, the series info is the one most people are interested in.