Warning: This will delete ALL certificates (including private keys), account keys, renewal configuration and log files. Don’t run this unless you have a good reason to!
You might also be interested in the config_changes or rollback subcommands for the apache plugin, allowing you to view or revert changes made to your apache configuration.
Off the top of my head, this should remove any traces:
rm -rf /path/to/your/git/clone/directory
rm -rf ~/.local/share/letsencrypt
rm -rf /etc/letsencrypt
rm -rf /var/log/letsencrypt
rm -rf /var/lib/letsencrypt
(Let me know if I missed anything!)