Yes, you should have made your own templates and overrides directories ...
What you can do is rename all of the current directories for:
/classic
to your own template name:
/your_new_template_name
customize the file:
/includes/templates/your_new_template_name/template_info.php
then, once all of the files are in the new directories for your new template, you should be able to reload the original /classic and all of its files to the server so that you now have a clean Classic Template and your own customized template ...
Be sure to backup your database and your site before making these changes and straightening out your files and directories ...