run::run() is pretty unwieldy. As a first step in improving it, this
commit pulls most of the argument parsing into the `config` module.
It also renames `Configuration` to `Config`, just to be easier to type.
Eventually, there will probably be a `crate` visibility specifier that
does the same thing as `pub(crate)`. This commit replaces `pub` with
`pub(crate)`, so when `crate` is available we can easily switch to it.
