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Kobo will update its database when you insert the card.
There isn't a file manager, you only get the database view. You can create collection/shelves on your own with those. If you're open to mods, my AutoShelf mod will create a collection for each folder, however it expects a USB connection since that's the most common case of seeing books added to the reader.
So even with this mod you'd still have to plug the Kobo to your PC, or use a dumb charger that isn't detected as charger by the Kobo and thus show the Connection popup window. So you can connect, and then tap on the screen to activate AutoShelf on disconnect.
If you're open to alternative reading software, koreader/coolreader come with file browsers I think...
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