We introduce a new package structure for Coq:

- `coq-core`: Coq's OCaml tools code and plugins
- `coq-stdlib`: Coq's stdlib [.vo files]
- `coq`: meta-package that pulls `coq-{core,stdlib}`

This has several advantages, in particular it allows to install Coq
without the stdlib which is useful in several scenarios, it also open
the door towards a versioning of the stdlib at the package level.

The main user-visible change is that Coq's ML development files now
live in `$lib/coq-core`, for compatibility in the regular build we
install a symlink and support both setups for a while.

Note that plugin developers and even `coq_makefile` should actually
rely on `ocamlfind` to locate Coq's OCaml libs as to be more robust.

There is a transient state where we actually look for both
`$coqlib/plugins` and `$coqlib/../coq-core/plugins` as to support
the non-ocamlfind plus custom variables.

This will be much improved once #13617 is merged (which requires this
PR first), then, we will introduce a `coq.boot` library so finally
`coqdep`, `coqchk`, etc... can share the same path setup code.

IMHO the plan should work fine.

This is similar to Constant and MutInd but for some reason this was was never
done. Such a patch makes the whole API more regular. We also deprecate the
legacy aliases.

This completes a pure Dune bootstrap of Coq.

There is still the question if we should modify `coqdep` so it does
output a dependency on `Init.Prelude.vo` in certain cases.

TODO: We still double-add `theories` and `plugins` [in coqinit and in
Dune], this should be easy to clean up.

Setting `libs_init_load_path` does give a correct build indeed;
however we still must call this for compatibility?

- Provide new helper functions in `Goptions` on the model of
  `declare_bool_option_and_ref`;

- Use these helper functions in many parts of the code base
  (encapsulates the corresponding references);

- Move almost all options from `declare_string_option` to
  `declare_stringopt_option` (only "Warnings" continue to use the
  former).  This means that these options now support `Unset` to get
  back to the default setting.  Note that there is a naming
  misalignment since `declare_int_option` is similar to
  `declare_stringopt_option` and supports `Unset`.  When "Warning" is
  eventually migrated to support `Unset` as well, we can remove
  `declare_string_option` and rename `declare_stringopt_option` to
  `declare_string_option`.

- For some vernac options and flags that have an equivalent
  command-line option or flag, implement it like the standard `-set`
  and `-unset`.

Add headers to a few files which were missing them.

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

The standard use is to repeat the option keywords in lowercase, which
is basically useless.

En passant add doc entry for Dump Arith.

We also remove trailing whitespace.

Script used:

```bash
for i in `find . -name '*.ml' -or -name '*.mli' -or -name '*.mlg'`; do expand -i "$i" | sponge "$i"; sed -e's/[[:space:]]*$//' -i.bak "$i"; done
```

This could be Prop (for compat with usual Coq), Set (for HoTT),
 or actually an arbitrary "i".

Take lower bound of universes into account in pretyping/engine

Reinstate proper elaboration of SProp <= l constraints:

replacing is_small with equality with lbound is _not_ semantics preserving!

lbound = Set

Elaborate template polymorphic inductives with lower bound Prop

This will make more constraints explicit

Check univ constraints with Prop as lower bound for template inductives

Restrict template polymorphic universes to those not bounded from below

Fixes #9294

fix suggested by Matthieu

Try second fix suggested by Matthieu

Take care of modifying elaboration for record declarations as well.

Rebase and export functions for debug

Remove exported functions used while debugging

Add a new typing flag "check_template" and option "-no-template-checl"

This parameterizes the new criterion on template polymorphic inductives
to allow bypassing it (necessary for backward compatibility).

Update checker to the new typing flags structure

Switch on the new template_check flag to allow old unsafe behavior in
indTyping.

This is the only change of code really impacting the kernel, together
with the commit implementing unbounded from below and parameterization
by the lower bound on universes.

Add deprecated option `Unset Template Check` allowing to make proof
scripts work with both 8.9 and 8.10 for a while

Fix `Template Check` option name and test it

Add `Unset Template Check` to Coq89.v

Cooking of inductives and template-check tests

Cleanup test-suite file for template check / universes(template) flags

cookind tests

Move test of `Unset Template Check` to the failure/ dir, but comment it
for now

Template test-suite test explanation

Overlays for PR 9918

Overlay for paramcoq

Add overlay for fiat_parsers (-no-template-check)

Add overlay for fiat_crypto_legacy

Update fiat-crypto legacy overlay

Now it points at the version that I plan on merging; I am hoping that doing this will guard against mistakes by adding an extra check that the target tested by Coq's CI on this branch works with the change I made.

Remove overlay that should no longer be necessary

The setting in the compat file should handle it

Remove now-merged fiat-crypto-legacy overlay

Update `Print Assumptions` to reflect the typing flag for template checking

Fix About and Print Assumptions for template poly, giving info on which
variables are actually polymorphic

Fix pretty printing to print global universe levels properly

Fix printing of template polymorphic universes

Fix pretty printing for template polymorphism on no universe

Fix interaction of template check and universes(template) flag

Fix indTyping to really check if there is any point in polymorphism: the
conclusion sort should be parameterized over at least one local universe

Indtyping fixes for template polymorphic Props

Allow explicit template polymorphism again

Adapt to new indTyping interface

Handle the case of template-polymorphic on no universes
correctly (morally Type0m univ represented as Prop).

Fix check of meaningfullness of template polymorphism in the kernel.

It is now done w.r.t the min_univ, the minimal universe inferred for the
inductive/record type, independently of the user-written annotation
which must only be larger than min_univ. This preserves compatibility
with UniMath and template-polymorphism as it has been implemented up-to
now.

Comment on identity non-template-polymorphism

Remove incorrect universes(template) attributes from ssr

simpl_fun can be meaningfully template-poly, as well as
pred_key (although the use is debatable: it could just
as well be in Prop).

Move `fun_of_simpl` coercion declaration out of section to respect
uniform inheritance

Remove incorrect uses of #[universes(template)] from the stdlib

Extraction of micromega changes due to moving an ind decl out of a section

Remove incorrect uses of #[universes(template)] from plugins

Fix test-suite files, removing incorrect #[universes(template)] attributes

Remove incorrect #[universes(template)] attributes in test-suite

Fix test-suite

Remove overlays as they have been merged upstream.