The CLI application is built using Seahorse, allowing for flexible and secure encryption/decryption of secret messages using Caesar's and Bacon's ciphers. The application can encrypt and decrypt input text with user-specified rotations and algorithms, as well as send encrypted ciphertexts to a specified WhatsApp recipient via Twilio's Programmable Messaging API. The application includes features such as command-line argument handling, flag parsing, and error messaging, making it suitable for secure communication among friends or colleagues.