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Calibre will create a copy of all your books in it's own location; the calibre library. Your original content will remain wherever it was. Don't make the common mistake of playing around with the files ) folders in the calibre location; accept it for what it is; a database totally managed / controlled by calibre.
Plugins come down to personal preferences. The only one I'd really recommend is the Kobo Utilities, namely because it provides an easy means to backup the database that the Kobo maintains of all content on the device.
Beyond that you enter one of the religious discussion points. Some people feel that they will only read epubs if they have been converted into the kepub format; others are very happy with the Epub format. The difference is the reading engine on the Kobo. Epubs use an older version of the Adobe RMSDK library, while kepubs use an engine whose name I forget but used to be called Access.
If you want kepub then you also require to install the Kobo Touch Extended plugin which will do the conversion on the fly as content is sent to the Kobo.
Sent from my Pixel 7a using Tapatalk
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