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I think it was my post you originally saw, where accessing the Home screen takes about 30 seconds for my collection of more than 1,700 books on the device. I do indeed use Calibre to manage my books, so that every book is actually in a folder (or to be correct a sub-folder) in the Documents directory.
Initially I thought it might be a problem that each book was also accompanied by a separate (but redundant) cover.jpg file and so I did a global deletion of them all. That saved me a hundred MB or so, but still didn't speed up Home screen access.
My current statistics, running a Properties check on the device from Windows 7, shows 1,711 files (i.e. ebooks), and 2,373 folders.
What I haven't done is run a fragmentation assessment utility on the Kindle -- but this is probably academic anyway given that most expert advice is not to defragment a SSD.
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