When upgrading a site, clone old site and immediately audit and clean the copy:
Content, taxonomies, blocks, media, and their respective types
User accounts, roles, plugins/modules, themes, etc.
You have the entire development period to discover anything that shouldn't have been deleted
Never load content files (images, documents, etc.) directly into the filesystem
No way to track such files to know if they're still in use or not
Always attach files to page objects (nodes) within the site
Simplicity, Abstraction, and the Modern Website: 10 Years Later