What are my options?
I think your best option is not to swim against the current. The vast majority of developers organize code in files and folders because people can easily understand hierarchies. Developer tools (IDEs and editors) have good search and fuzzy find built-in so you don't have to click through folder hierarchies to find a file, or find where a function gets defined.
They have an "image" which contains everything (including the system-provided libraries), in a single file, and rely on the development environment to navigate to classes,functions, etc.