[cli] Refactor directory.

I refactored the directory into the core `cli` commands and the utility systems processes. I think the new file-names make it easier to find the functions you are looking for. Ideally, we should have directories like `util` and `core` and then a `main.ml` file at the top-level that gets build. My fork will experiment with this idea. But I think this is a bit better for now.

@Bennn Let me know if you think that any of the files should be moved around. This should directory structure should also be good for addressing #9.