[api] Put modules in order in API.{mli,ml}

We sort the dependency graph of API by following a logical declaration
order in `API.{ml,mli}` related to the actual dependency order of Coq
modules.

Things are a bit tricky here as Coq itself relies on the fact that
OCaml treats module interface and implementation separately
dependency-wise; however, when resorting module alias the design seems
to become more coupled.

Currently, API exposes both "namespaces", asserting a large number of
type equality between them, however the `API` namespace is not
self-contained.

In particular, this is a first step to solve problems such as
`Summary.frozen` being used in `API.mli` but not declared by the
`API.Summary` module, etc... In general we follow the invariant that a
type used in `API` must have been declared before.

Keep in mind that OCaml upstream has warned that it maybe tricky to
alias objects in this way. In particular, after API the old `mli` only
files have become full compilation units so we may want to be more
careful here.

The more "correct" declaration order allows us to remove the
`API.Prelude` module, as well as some other declarations that I
consider as spurious.

We still maintain the large number of type aliases which will be
removed in a future patch.

We follow linking order except for files in `intf`, which are
conceptually wrongly placed in the linking hierarchy but this doesn't
matter as the files don't contain any implementation.

We also move a couple of `.mli` only files to `.ml` so we are
consistent, and correct their linking order in `mllib`, even if that
doesn't matter as such `.ml`-only files contain no implementations.

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