Chris Wanstrath describes the process of optimizing GitHub's deployment system to significantly reduce deployment time from 15 minutes to 14 seconds. Initially, GitHub used a complex Capistrano setup with 400 lines of code and several custom tasks, which was effective for SVN but inefficient for Git. Wanstrath explored alternatives like Vlad, Heroku's Rush, and Fabric, but found them unsuitable due to their complexity or incompatibility with GitHub's needs. Inspired by Fabric, Wanstrath restructured the deployment process by splitting the deploy script into smaller, focused components and simplifying tasks to reduce overhead. By eliminating timestamp directories and using a more Git-based approach with Capistrano's capabilities, he streamlined deployments. Additionally, he improved efficiency by minimizing and bundling JavaScript and CSS on servers rather than locally, further accelerating the deployment process.