We could certainly run it from within the framework, and cache the results in whatever cache engine is setup instead of a file (for performance) - I'd be a little concerned about the performance hit of testing the controller files for revisions essentially on every hit.
I can definitely see a use in the cortex plugin - thats a good idea but you'd need to devise a way to proxy the setup calls out to the generated code - i.e. a hook o call INTO your cortex class form generated code to apply the effect of the annotations.
I am very comfortable with dev-time tooling and file watchers - and its very speedy so the regeneration when I save changes to a controller is negligible - I'm a little wary of run-time generation because it isn't performant, and in practice controllers, model files, etc don't change, except in development. But I wouldn't make run-time integration a condition of using annotations in cortex in any case. It would still be useful as a dev-time tool. I use it as a gulp task, but it could be executed by any task runner or ide file-watcher (i've used it as a file watcher in PHPStorm for example - in both cases I have it watch just the files of interest - eg. my controller directory)
I'm happy to collaborate on some ideas like that - resulting in a nice suite of annotations to augment F3 and ease development. In l=the latest revision I generalized the tag recognition in order to support PSR-5, but the whole tool can be architected to have specific tag type handlers, i.e. a plug in architecture to enable expansion.
Let me know your thoughts!
Rich