How to move drupal into a subdirectory so non-drupal content works in the original folder?
If your non-drupal files are just a few and are static content (just plain HTML files or similar) you can create symbolic links in the root Drupal foolder that point to your non-drupal files. 

Webserver (Apache at least) will serve those files if the URL points to them, instead of call index.php with the URL rewriten into params.

This way if you accidentally delete root Drupal directory (for example, using an automatic core update) you only have to put the simbolic links again, not all your non-drupal files.