All of our shared, semi-dedicated, and reseller hosting plans include a feature known as AutoSSL. AutoSSL automatically installs a signed, trusted, and secure SSL certificate on all domains hosted from your account. These SSL certificates are issued by Let's Encrypt.
When Let's Encrypt installs your certificate(s) it authenticates the domain through the ACME Protocol and domain validation. The Let’s Encrypt CA will look at the domain name being requested and issue one or more sets of challenges. This is why the 'well-known' and 'acme-challenge' directories are created as the validation files are placed in those directories.
The directories are completely safe and should not be removed. Further technical details about this validation can be found at https://letsencrypt.org/how-it-works/