Yes, manually specified file modules can be stored in a file, but I don’t love the idea of checking it for changes all the time or trying to figure out how to invalidate a cache.
Upon reflection, it seems quite possible to just have the parser store includes that it finds in-memory and on the fly. It shouldn’t affect performance much. It also has the advantage of working if the root module including a particular file changes (the change will be picked up on a re-parse of the new root module). I think that only leaves the corner case of a file going from being an include-only part of a module to something independent or a root module of its own.
I have to give some thought to how to correctly implement this feature, but it does seem like something I can add.
Thanks for the suggestion!