Use FromClean more.

The `FromClean` trait is used a lot for converting to rustdoc-json
format. But it's not used universally; there are still some ad hoc
functions and methods for converting. This commit fixes this
inconsistency by using `FromClean` more.

The commit also introduces `FromClean` for `Box` and `Option`. This lets
a lot of `as_ref` and `map` calls be removed in favour of simple
`into_json` calls.

Author: nnethercote