How can I clear all contacts (as if they never existed) without touching any CiviCRM settings?
I would suggest to perform deletion of contact from UI and then reseting the auto increment value through mysql command. Truncating database might loose contact that are not suppose to be deleted like logged in contact id or Default organization contact id or they might be possible to have orphan data for contacts if we directly truncate the table. Here is what i would do


Find Contact
Select All contact
From Action list i will select 'Delete Contact permanently'


Shell in for mysql or in phymyadmin through web and run ALTER TABLE civicrm_contact AUTO_INCREMENT = 1 


  Note: Backup database before deleting contacts.


HTH

Pradeep