docs: add Doxygen/Breathe infrastructure for C++ API reference

[CV-GPhL]

Summary

Adds the build infrastructure needed to generate a C++ API reference from
Doxygen comments in `include/gemmi/*.hpp` and render it within the existing
Sphinx/readthedocs documentation site.

This is PR 1 of a planned series of 10 PRs. PRs 2–10 add full Doxygen
comments to all public headers and depend on this PR being merged first —
they will expand `docs/api.rst` and have no meaning without the build pipeline
established here.

What this PR does

• Adds `docs/Doxyfile`: Doxygen configuration producing XML consumed by Breathe.
  Internal/data-only headers (`ace_*.hpp`, `acedrg_tables.hpp`, `mc_tables.hpp`,
  `eig3.hpp`, `cc_adj.hpp`, `ccp4ener.hpp`) are excluded.
• Extends `docs/conf.py`: runs Doxygen as a subprocess before the Sphinx build,
  adds the `breathe` Sphinx extension and its configuration.
• Adds `docs/api.rst`: a stub C++ API reference page included in the existing toctree.
  This stub will grow with each subsequent PR in this series.
• Updates `docs/index.rst`: replaces the external link to `project-gemmi.github.io/cxx-api/`
  with an internal link to the new `api.rst` page.
• Updates `docs/requirements.txt` and `.readthedocs.yaml` to install `breathe` and `doxygen`.

Planned PR series (all depend on this PR)

PR	Content
1 (this PR)	Build infrastructure
2	Core structures: `model.hpp`, `unitcell.hpp`, `symmetry.hpp`, `metadata.hpp`, `elem.hpp`, `seqid.hpp`, `resinfo.hpp`, `small.hpp`
3	CIF: `cif.hpp`, `cifdoc.hpp`, `read_cif.hpp`, `to_cif.hpp`, `to_json.hpp`, `json.hpp`, `numb.hpp`, `ddl.hpp`
4	Structure I/O: `mmcif.hpp`, `mmread.hpp`, `pdb.hpp`, `to_mmcif.hpp`, `to_pdb.hpp`, `mmdb.hpp`, `crd.hpp`, …
5	Reflection data: `mtz.hpp`, `refln.hpp`, `cif2mtz.hpp`, `mtz2cif.hpp`, `xds_ascii.hpp`, `binner.hpp`, …
6	Maps/grids: `grid.hpp`, `ccp4.hpp`, `dencalc.hpp`, `fourier.hpp`, `solmask.hpp`, …
7	Calculations: `calculate.hpp`, `neighbor.hpp`, `sfcalc.hpp`, `align.hpp`, `select.hpp`, …
8	Chemistry/monomer: `chemcomp.hpp`, `monlib.hpp`, `topo.hpp`, `riding_h.hpp`, …
9	Scattering/math: `formfact.hpp`, `it92.hpp`, `fprime.hpp`, `math.hpp`, `cellred.hpp`, …
10	I/O utilities: `dirwalk.hpp`, `fileutil.hpp`, `gz.hpp`, `util.hpp`, `span.hpp`, …

Relationship to PR #402

This PR is the first in a series building on Paul Emsley's PR #402 (pemsley). As requested
by @wojdyr in the discussion there, the Doxygen configuration lives under `docs/` alongside
the existing Sphinx configuration rather than under `include/gemmi/`. The `doxy-sphinx/`
directory from PR #402 is not included here.

Build verification

```
cd docs && make html # runs Doxygen then Sphinx; api.html ~600KB
```

Verified locally: doxygen 1.9.8, breathe 4.36.0, Sphinx 9.1.0, ubuntu-24.04.

Test plan

• Confirm readthedocs build passes with `apt_packages: [doxygen]`
• Confirm `docs/api.html` renders without Breathe errors
• Confirm `docs/_doxygen/` is not committed (gitignored)

[wojdyr]

[wojdyr]

somehow i'm notable to merge it

[wojdyr]

i'mtrying tomerge sll these PRs, but I'm not able

[wojdyr]

@keitaroyam can you try?

[keitaroyam]

What's happening? Why so many PRs?

[wojdyr]

Clemens

What's happening? Why so many PRs?

Clemens adds Doxygen comments

[CV-GPhL]

Sorry about that barrage of PRs ... I thought it made more sense to split them into (reasonably) logical blocks since it is/was quite a lot.