I really like Calibre a lot and use it to manage my fanfic collection to read on my Kindle. In fact, besides converted academic PDFs, fanfic is pretty much the only thing I read on my Kindle.
Like you, I had a big stash of old fanfic on my hard drive from decades gone by; mostly in HTML format, but some PDF, RTF, and TXT. I used Calibre to batch convert them all to MOBI for the Kindle. Calibre's batch metadata editing feature came in handy as well, since I batch converted old fic by fandom and then updated the tags in a big batch. (I agree with nonniemous that TXT isn't the best format to convert from, but it works well enough...you just lose some formatting like italics and bold.) I also like the Kindle collections plug-in that's available so I can group fanfic into specific fantoms and genres (e.g. Crossovers) on my Kindle so I don't have to sort though the fic alphabetically by title or author which is a huge win.
Anyway, yeah, you're right, Calibre maintains its library in directories/sub directories on a per author/story basis. But I guess this doesn't bother me because: 1) even binary format fic files are small in comparison to other media types (e.g. video files) and I have multiple huge hard drives so I won't ever run out of space, and 2) I keep backups of the old files and any new files in my original directory layout anyway. That way, if I ever stop using Calibre, I'll still have all my files stored in my original directory hierarchy and I'll be able to just delete the Calibre library. Additionally, since I use Calibre to upload stuff to my Kindle, the Calibre library and its files have to stay as they are for that functionality to work.
If you only want to use Calibre to convert files and not manage your e-library, then unless you have the skill to write a script in Python/Java/Perl/awk/whatever, I'm not sure there is any way to batch-copy the files out of the Calibre directory structure and move them to the directory you want.
Writing shell scripts isn't really difficult, though, so you might want to try that anyway just for fun. Simply type "writing shell scripts in [Python/Perl/bash/etc.]" into google and you'll find a lot of good suggestions and tutorials.
Two last points: Calibre does allow you to move your library to a different location than its default. And you can export subsets of your library collection to your hard drive in a user-defined directory hierarchy (which might be a way to do what you want without writing scripts). Information about those features and others that might be useful are located here and here
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Like you, I had a big stash of old fanfic on my hard drive from decades gone by; mostly in HTML format, but some PDF, RTF, and TXT. I used Calibre to batch convert them all to MOBI for the Kindle. Calibre's batch metadata editing feature came in handy as well, since I batch converted old fic by fandom and then updated the tags in a big batch. (I agree with
Anyway, yeah, you're right, Calibre maintains its library in directories/sub directories on a per author/story basis. But I guess this doesn't bother me because:
1) even binary format fic files are small in comparison to other media types (e.g. video files) and I have multiple huge hard drives so I won't ever run out of space, and
2) I keep backups of the old files and any new files in my original directory layout anyway. That way, if I ever stop using Calibre, I'll still have all my files stored in my original directory hierarchy and I'll be able to just delete the Calibre library. Additionally, since I use Calibre to upload stuff to my Kindle, the Calibre library and its files have to stay as they are for that functionality to work.
If you only want to use Calibre to convert files and not manage your e-library, then unless you have the skill to write a script in Python/Java/Perl/awk/whatever, I'm not sure there is any way to batch-copy the files out of the Calibre directory structure and move them to the directory you want.
Writing shell scripts isn't really difficult, though, so you might want to try that anyway just for fun. Simply type "writing shell scripts in [Python/Perl/bash/etc.]" into google and you'll find a lot of good suggestions and tutorials.
Two last points: Calibre does allow you to move your library to a different location than its default. And you can export subsets of your library collection to your hard drive in a user-defined directory hierarchy (which might be a way to do what you want without writing scripts). Information about those features and others that might be useful are located here and here
Hope this helps!