docs: full Doxygen API documentation for structure I/O

[CV-GPhL]

Summary

This PR adds complete Doxygen API documentation for Gemmi's structure file I/O layer, covering 10 headers:

• mmcif.hpp — structure reading from mmCIF (make_structure, make_structure_from_block, ChemCompModel)
• mmread.hpp — universal structure reader (read_structure_file, format detection)
• mmread_gz.hpp — gzip-aware reading wrappers
• pdb.hpp — PDB-format reading (including hybrid-36, REMARK 290 symmetry)
• to_mmcif.hpp — structure writing to mmCIF (MmcifOutputGroups with 31 output categories)
• to_pdb.hpp — structure writing to PDB (PdbWriteOptions, use_hetatm classification)
• crd.hpp — Refmac CRD preparation (setup_for_crd, prepare_refmac_crd)
• smcif.hpp — small-molecule CIF reading/writing (fractional coordinates, SmallStructure)
• mmdb.hpp — CCP4 MMDB interop layer (copy_to_mmdb, copy_from_mmdb and helpers)
• pirfasta.hpp — PIR/FASTA sequence format (is_pir_format, read_pir_or_fasta)

Documentation standard

• /// triple-slash Doxygen comments throughout
• Every public entity has @brief; non-obvious parameters have @param/@return/@throws/@tparam
• Semantics verified against implementations (e.g., save_doc move semantics, use_hetatm three-tier classification, REMARK 290 triplet notation, fractional vs Cartesian coordinates)

Dependencies

This PR depends on PR #413 (Doxygen/Breathe infrastructure) being merged first.

It follows PR #414 (core data structures) and PR #415 (CIF handling) in the documentation series.

Series context

This is PR 4 of a planned series of 10 PRs adding incremental API documentation:

PR	Branch	Content
#413	api-docs/infra	Build infrastructure (Doxyfile, conf.py, api.rst, readthedocs)
#414	api-docs/core-structures	model.hpp, unitcell.hpp, symmetry.hpp, metadata.hpp, elem.hpp, seqid.hpp, resinfo.hpp, small.hpp
#415	api-docs/cif	cif.hpp, cifdoc.hpp, read_cif.hpp, to_cif.hpp, to_json.hpp, json.hpp, numb.hpp, ddl.hpp
This PR	api-docs/structure-io	mmcif.hpp, mmread.hpp, mmread_gz.hpp, pdb.hpp, to_mmcif.hpp, to_pdb.hpp, crd.hpp, smcif.hpp, mmdb.hpp, pirfasta.hpp
PR 5	api-docs/reflection	mtz.hpp, refln.hpp, cif2mtz.hpp, mtz2cif.hpp, and related
PR 6	api-docs/maps-grids	grid.hpp, ccp4.hpp, dencalc.hpp, fourier.hpp, and related
PR 7	api-docs/calculations	calculate.hpp, neighbor.hpp, sfcalc.hpp, align.hpp, and related
PR 8	api-docs/chemistry	chemcomp.hpp, monlib.hpp, topo.hpp, and related
PR 9	api-docs/scattering-math	formfact.hpp, math.hpp, cellred.hpp, and related
PR 10	api-docs/io-utils	fileutil.hpp, gz.hpp, util.hpp, logger.hpp, and related

Attribution

Builds on and credits prior work in PR #402 (Paul Emsley / pemsley). All comments audited/rewritten where needed against actual implementations.