When copying the files of a Drupal install, do not forget to copy Drupal's
.htaccess file. If you've had the vexing problem where a site you've just manipulated has clean URLs turned on but they suddenly don't work, this may well be the reason. It took me fixing this problem many times before I realized what was going on.
You make a directory for a new site,
cd to the new directory, and use
drush to download Drupal.
% mkdir mynewsite
% cd mynewsite
% drush dl drupal