Before this turns into a full blown flame war, let me explain something about how calibre works since it is something most people are not used to. For decades, computers have used the folder and filename system to organize data files. It works but it actually is very inefficient, especially if one has a file that can be classified in more than one place. The only two options in the latter scenario is to either file duplicate files or to create shortcuts to the original file. The latter option has the advantage that any changes to the original will be seen when accessed through a shortcut whereas with duplicate files, one would have to run down every duplicate to duplicate the change. A downside to both options is if one wants to delete a file, one would have to run down every duplicate file or shortcut and delete them all. It is a simple system needing only the Operating System to support it but it is very inefficient.
A better system for file organization is to attach metadata, also known as tags, to each file then use software to list and find the files. This way, a file can be classifed in an unlimited (depending on how the software was programmed) number of categories. Menus can be generated for each category allowing fast and easy access to each file. Many music management programs use a system similar to this. Some will keep the metadata within the program (which tends to limit its flexibility), some will attach the metadata directly to the files (which changes the file; not necessarilly a good thing), and others will put the metadata in a separate file in a folder with the files (probably the most efficient way to do this). The latter is what calibre does.
Often, newcomers to calibre have a hard time grasping that calibre is not just a book cataloging program that happens to do conversions but is a complete book management system. Once calibre has copied a book to its folder (calibre doesn't touch or move the original file), there is no longer any need to directly access the book through the folder/filename system (in fact, messing around in calibre's folders could cause problems). Anything you could have done with the folder/filename system can be done from within calibre. In fact, you can do far more from within calibre than you can from any folder/filename setup. You just have to let go of the old and adopt the new. Instead of fighting calibre, let it work for you.
One of the nice things about calibre is this forum where people can go for help when having problems understanding it (calibre is a complex program. But you do have to ask with an open mind. We have had so many people come here insisting, often belligerently, that they need to keep their original folder/filename structure that some of the fold here get their backs up when it happens. Approach them nicely with an open mind and they will bend over backwards for you. I'm an idiot when it comes to computers and software and have to be walked through every step like a small child (which is sad since I'm large and old). If I get confused along the way, I just say so and the folks here will do whatever they can to help me.
I tried many programs prior to calibre (and sice then, too) and I haven't found any that were able to meet my needs as well as calibre, not to mention the incredible support system.
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