All you wanted to know about the Notes directory structure is explained here: “Understanding the IBM Lotus Notes 8.5.x client directory structure” via Stephan Wissel.
“This article explains the changes that were introduced in the IBM Lotus Notes 8.5 File System installation and describes them with respect to the installation, setup/launch/run, and uninstall phases in the client’s life cycle. Also included are answers to some FAQs on the client file system.”