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Like Bee-Tee-Ess, I tried collections and ran into issues with slowness when they multiplied like rabbits. My personal answer was to drop all collections/shelves though they do tend to return like stubborn zombies in favour of using search. Given that Kobo's search uses series name, author name and book name and that Calibre allows for the capability to have your ebooks named with series info embedded in the name, it works quite well for me. It was a bit of wrench giving up worrying about file systems, directory layouts, etc. but after a while, I found that I no longer miss them.
Since Koreader now supports using the Calibre metadata files for search as well, it makes Koreader easier for me to use without having to revert to the old method of searching down the directory tree for the ebook I want to read.
Regards,
David
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