[build] Consolidate stdlib's .v files under a single directory.

Currently, `.v` under the `Coq.` prefix are found in both `theories`
and `plugins`. Usually these two directories are merged by special
loadpath code that allows double-binding of the prefix.

This adds some complexity to the build and loadpath system; and in
particular, it prevents from handling the `Coq.*` prefix in the
simple, `-R theories Coq` standard way.

We thus move all `.v` files to theories, leaving `plugins` as an
OCaml-only directory, and modify accordingly the loadpath / build
infrastructure.

Note that in general `plugins/foo/Foo.v` was not self-contained, in
the sense that it depended on files in `theories` and files in
`theories` depended on it; moreover, Coq saw all these files as
belonging to the same namespace so it didn't really care where they
lived.

This could also imply a performance gain as we now effectively
traverse less directories when locating a library.

See also discussion in #10003

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