Security and privacy on the internet is generally achieved using public key cryptography, and SSL or TLS. Getting a public key (also called a certificate) signed by a trusted source has been a fairly expensive exercise for small company, hobbyists, and open source projects. More recently, public knowledge of mass internet servalience has pushed for more security of web traffic (in particular).
Enter Let's Encrypt. It is a certificate authority that signs certificates for free, making secure websites much more widely available. As part of keeping it free and in a way to reduce abuse, the certificates issued are only valid for a short time, currently 3 months. To help manage the certificates and simplify the validation of the domain name they apply to, let's encrypt has written software that (mostly) automates the process.