Josh Miller wrote:
Is there anyone else worried that the Drupal folder structure encourages users to drop modules or themes into the wrong place? Wouldn't you like to have a folder structure that separates core from the rest of the customizable sites folder?
This discussion has been had in the issue queue: http://drupal.org/node/523934 (That's just one, it's been marked dup of another, I think, though it was barely a dup)
