I have ~7000 books on my AuraHD and I still use a regular file/naming system. I did test the metadata search function, and it is really neat, but I don't use it.
Another new feature in Koreader, the OPDS support is very cool, as well. You can acquire books from OPDS catalogs using Koreader and then read them using Coolreader, if you wanted to.
Luck;
Ken
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