Humbledore, I agree. Although I'm very happy that "move all files" became available in the first place it's not entirely logical
There are 2 ways around it that I use (one of which glynor didn't mention)
1. Don't import images or ancillary files. This is easiest to achieve by using an "incoming" folder that is image free, then moving into the main library using the RMC. My incoming folder ONLY sees flac and mp3, nothing else gets in
The files will move
2. Tag all the ancillary files with album and artist the same as the album itself. This is most easily achieved by CTRL-C, CTRL shift V to paste tags only
If the files have the same album and artist tags they will move.
I'd love for this to be a bit more intuitive but at the same time it's forced me into a workflow (incoming folder) that is much better anyway. All in all the change saved me months of work moving tens of thousands of albums into a complete new structure (yay JRiver thanks!), it just took some getting used to
Not really an option, but something to mention, but if you save in the file itself the cover image becomes only useful for external programs (and many will read the internal file). I save logs and booklets etc so it's not useful for me but if you're a cover art only guy, it may be worth saving to the file and to a separate directory (cover art) and not worry about them at all