Let's do a small wrap up of the main concepts seen so far. Each directory under store/ or tags/ is a tag. If you copy a file under the store/ directory it gets tagged. You can establish relations between tags using the relations/ directory. If a tag A includes the tag B all the files tagged as B will show up in store/A/@/ as well.
So far, so good. Now imagine that you tagged your mp3 library by band name and then organized the band tags by genre. In the end you included all the genre tags in music. Something like:
$ cp the_number_of_the_beast.mp3 ~/myfiles/store/iron_maiden/@
[... other files too ...]
$ mkdir ~/myfiles/relations/heavy_metal/includes/iron_maiden/
[... other bands too ...]
$ mkdir ~/myfiles/relations/music/includes/heavy_metal/
$ mkdir ~/myfiles/relations/music/includes/jazz/
$ mkdir ~/myfiles/relations/music/includes/classical/
$ mkdir ~/myfiles/relations/music/includes/piano/
[... other genres too ...]
$ ls ~/myfiles/store/music/@
[... your whole library here ...]
Amazing! All your files in one place, without having to tag them as music one by one. Now you can for example open ~/myfiles/store/heavy_metal/@/ with your favorite audio player to listen to all your heavy metal collection, excluding those fine jazz sessions or Bach's fugues. You start the application, click on the_number_of_the_beast.mp3 and... the smooth timbre of a piano spreads in the room. What the hell happened to distorted guitars?
Oh, sure, now you remember: that version of The Number of the Beast is a nice tribute cover by a classical piano player. Better move it to ~/myfiles/store/classical/piano/@:
$ mv ~/myfiles/store/music/@/the_number_of_the_beast.mp3 ~/myfiles/store/classical/piano/@
You give the move command and... the file is still there?!?!
Of course it is, because the reasoner knows that the music tag includes both classical and piano tags too, so your file still features in the results of store/music/@. But how could you know that moving (re-tagging) the file happened? The reasoner prevents you from being sure.
The answer is: ask the reasoner to not step in!
If you end a query with the special @@/ marker, the reasoner doesn't get involved, so only the files with an explicit tagging are returned. In example, if you list store/music/@@/, no files are listed, because music is by itself totally empty (no file has been tagged as music). The very same happens if you list store/heavy_metal/@@/. But if you list store/iron_maiden/@@/, all your Iron Maiden songs are there.
The @@/ marker is usually applied to single tag queries, like store/iron_maiden/@@/ to ease the re-tagging process.