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kingseesar - some people use calibre as a catalog only, and leave the book files where they are. Hopefully one of them will drop by and give some guidance. But here are some thoughts
Firstly have a browse through this ==>>
Calibre command line interface
If you want calibre to extract metadata from the format files (EPUB, PDF etc) as it adds (i.e. you've checked Preferences->Add books->Read metadata from file contents...) then you will have to add the format files - but you do not have to keep them in the library. Once the book is added you can remove the format files - you should use calibre's Remove Formats feature to do this rather than your file manager. Using the file manager will result in the calibre library's database and its folder/file contents being inconsistent which is best avoided,
Or, you could use the ebook-meta command to extract the metadata from the existing files into OPF files and add those to the calibre GUI. Calibre's going to retain an OPF anyway, they are used by its database restore feature.
On Windows you could add a shortcut file to a book that references the current location. Alternatively you could put a hyperlink to the existing format file (folder) into the Comments column (or a similar custom column) or into an Arbitrary Identifier. The advantage of using shortcuts is that if you rename or move a shortcut target, Windows will try to repair any LNK files that refer to it - providing you haven't disabled the DLT Service. AFAIK there is no similar feature to repair broken file system URIs - on Windows, OSX or Linux.
Using shortcut files or URLs (file:\\\blah de blah) precludes the use of some of the GUI features - particularly those relating to devices. However many features are also available from the command line - eg conversion and the aforementioned ebook-meta command. The calibredb command also has many useful features.
One of the main attributes of calibre is its flexibility - i.e. there are many ways to skin a cat, other than dragging it backwards through a keyhole
Added - have you taken the time to watch the
Video Tutorials. I found them very useful when I started to use calibre - I'm someone who despises video 'instructions'. Watch a segment, then practise it on a test library, if it doesn't work as expected - re-wind/re-play/re-practise.
BR