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I have 10,000+ books in my library. I use Calibre to keep some sort of overview, and use its Save to Disk feature to build and populate the folder structure I want on my reader.
The latest version of Calibre still needs several minutes to start with a large library like this, and I find that Save to Disk is very slow (although part of the problem is my rather old computer). For the rest I have no performance problem. Searching and filtering is very fast.
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