Quote:
Originally Posted by Riqiv
Thank you Peter, for the prompt and polite response 
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Polite question almost always gets a prompt and polite answer here at this forum ;-)
The thing is, that Calibre wants to manage its own library files. Some people make a mistake that when the Calibre starts for the first time and asks where it is supposed to put the library, they do not select (or create in place) AN EMPTY folder/directory.
There have been countless discussions here asking the author of Calibre - Kovid Goyal - to change the structure of that folder to suit some users.
You are not supposed to mess with that Calibre Library folder, except, of course for regular backup of the entire thing. For many reasons it is even better to use "save to disk" function in Calibre instead of looking up the files manually. When you use "save to disk" function Calibre makes sure there will be the most recent metadata bundled inside the the book file. Calibre Library folder is supposed to be a "black box" to you, and you should access your files using Calibre graphical interface. The interface has quite a few tools and features that will let you manipulate your books.
Is somebody chooses his existing folder with books as a base for the Calibre Library and then starts importing books, the result is an UGLY (and, as you have seen, dangerous) mess. Because Calibre will make a copy of each of imported books there in its own directory structure. This thread and other ones have prompted another improvement to Calibre. The recent versions will refuse to place Library to a folder that is not empty. Kovid listens to the community and every Friday there is a new version with a new cool feature or improvement.
As for the comandline tools.
Calibre is very, VERY, versatile tool. It can convert between many ebook formats, it can download ebook metadata from the net, it can use so-called "recipes" to download the contents of your favourite blog, site, on-line newspaper and make a very nice ebook of it and push it to your reading device (of course, your device must support receiving emails or whatever for pushing to function). Calibre can even turn itself into a very nice web server and let you browse the library over the net from another PC at home or from device.
Many of those features can be used without using the Grafical User Interface - GUI. Calibre consists of many independent parts and there are people that like to use, for example "convert" CommandLine command to convert books.