I understand that you probably don't want to duplicate your collection but 25 GB is nothing in terms of storage. So no reason you can't have both.
When I started using calibre I was in the same boat. I imported books converted them, saved them to 'my' structure and deleted them.
Unfortunately I found myself doing this time and time again. Decide I want the series first in the filename, do again. Decide, no that is not right, author first, do again. Metadata wrong, do again.
I bit the bullet and imported all of the books (extreme pain but I got it done)
Took me quite a while to update and check metadata and decide how I wanted my books to
appear on my ereaders. but this was actually easier as time went on.
Like you I could always find my books and the ways of calibre were not so apparently advantageous at first.
Now it is in my mind the only way to go.
I can find a book or a group of books in a second or two (I am sure I could do that with the other file structure in less than a minute as well, perhaps as fast even)
I can store my own information for each book in calibre using either predefined or custom columns.
I can send the books to my various ereaders in whatever manner I chose, put them instantaneously in shelves or collections with very little intervention and if I want my collections different it only takes a very short time to accomplish this. A minute for me and maybe 3 minutes for calibre to make the changes. I don't have to send the books again, just change the driver config.
While many deplore calibre's file structure, for my needs it is as good as any. I often chose books based on genre. Many authors write in several genres. Elmore Leonard writes mysteries and westerns for example. If I had genre as my top level folder, I would need a subfolder for each author in each genre. If I chose authors as the top level I could need a genre subfolder for each level. What to do? With calibre I just need to categorize the book in my genre column. If I wanted to have a genre collection and an author collection without picking each author/genre one at a time and adding them, I could do this easily. Of course if you do not categorize your books this would have no value.
Basically with calibre I have the information I want all in one spot. I don't want the opf files or the cover.jpg file, but I am not overly upset by them. I do like the original file option so all of my data is pretty well doubled, but that is a matter of choice.
Helen
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