Not filesystems, file formats.
My preference is to always keep the original format, as the master -- to prevent lossiness in case I intend to later edit or anything.
Disk space is cheap, and ebooks are small.
Tags is a common classification method, you cannot go wrong there --- especially if it makes sense and works for you.
(Well, as much as anything is, I find title/author/series to be all I need and anything else just confuses me. I nuke tags from orbit.
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