Thank you for the quick reply and the advice BR. I don't go looking at those files, but I do think about them. My computer is getting old (as am I) and I wanted to try and make it a little easier on her. I have over 8,000 books, which means an additional 16,000 files. People who say that shouldn't affect how a computer runs don't have a low-end 5 year old clunker with less than 4 GB over working RAM. I also back up my library online, and the only thing slower at indexing files than my Samsung is Google Drive. Like I said before, I knew the files where there for a reason, I just wanted to see to what degree they were necessary.
I also wanted to thank you for actually answering my question. I found plenty of people asking the same question I did in other posts, but they were all responded to by the same people who "argue that you shouldn't even be looking...". I think people forget sometimes that the reason we are here talking about a program like calibre, is because Kovid is one of those guys that went looking.
And finally, the link to the FAQ you sent works for me as well, but that is not the same one you click on when you go to MobileRead Forums > E-Book Software > Calibre > New to calibre? Start Here. That FAQ link sends you to:
http://calibre-ebook.com/user_manual/faq.html .
Thanks again BetterRed. See ya 'round the book shelves.
2wr3ckl3ss