How to get drupal to remove /drupal/ from all the links on the website
The entry in the .htaccess file you should uncomment is the /drupal one: 

  # Modify the RewriteBase if you are using Drupal in a subdirectory or in a
  # VirtualDocumentRoot and the rewrite rules are not working properly.
  # For example if your site is at http://example.com/drupal uncomment and
  # modify the following line:
  RewriteBase /drupal