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Suspenders and belt are a lot of leather.
Once you put it into Calibre, you don't really need to keep the original source files. Calibre will copy your file, and keep any formats that you convert it to, in a well-organized directory system.
If you put in good metadata, and tag properly, for each book you would then manage everything from Calibre, instead of trying to manage the directory system yourself. In fact, once you give a book to Calibre, it helps to think of Calibre's system as a "black box" that you don't go in and mess with.
Calibre gives you a lot of tools for managing your books, but you should commit to it, and let it do its thing.
You don't have to delete the source files -- you can do whatever you want. Once you have worked with it long enough, though, I expect that you'll see that they are really redundant (especially if you don't want to manually sort them.)
m a r
ps: it can be overwhelming, if you have thousands of books. I'm working through similar issues myself.
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