Yeah, it's a good thought, and Brad has thought about it. The main problem with it is that it would be really hard to change the existing system. The way comics are stored on the server actually has the image URLs hardcoded into it, so moving them to different directories would fuck it up completely. To fix it, Brad would have to do a find and replace of _all_ the image URLs in _all_ the comics in the archive. That's a couple hundred images and getting on toward half a million comics.
Brad wrote the current system back when there were only a few thousand comics and a fraction of the current characters and backgrounds. At that time most art was kindly donated by friends of his with webcomics, so out of respect for them he classified the art according to its source (Diesel Sweeties, Goats, When I Grow Up, etc).
Then... well, I did some art. I did a handful at a time, submitting new characters in trickles. Since all the other art was from existing comics, Brad put my stuff in a "dexx" category, classifying them by source and style rather than character type.
Anyway, it's a good idea, and you're right - it would be easier, especially for new users. Trouble is, it would now be a bitch to change. Maybe Brad will think of an easy way to do it, but don't hold your breath.
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