docs: replace fabricated API stubs with real autodoc (D11)

[nceglia]

Summary

• The five docs/api/*.md pages were hand-written code blocks with pass bodies documenting an API that doesn't exist — global_joint_distribution, get_clones, get_phenotypes, normalize_distribution, TCRIModel.save/load, n_latent=10, fabricated signatures. Wrong docs are worse than none.
• Replaced all five (model, metrics, preprocessing, plotting, utils) with MyST eval-rst autodoc directives bound to the canonical modules, so the reference is generated from live code.
• automodule documents only members defined in each module, which neatly resolves the from .._X import * namespace pollution: numpy/pandas and cross-module re-exports are skipped, so each function appears once on its home page.

conf.py

• autodoc_default_options (members / undoc-members / show-inheritance) so the reference is complete now, before D1 docstrings land.
• add_module_names = False for clean signatures (joint_distribution(...), not tcri.preprocessing._preprocessing.joint_distribution(...)).
• autosummary_generate = True.
• Dropped the display_version theme option (unsupported in current sphinx_rtd_theme).

Also

• Fixed the ridge_delta_entropy docstring (ASCII diagram → RST literal block) so the build is warning-free.

Verification

• python -m sphinx -b html docs <out> → build succeeded, 0 warnings.
• Confirmed the real API renders (joint_distribution_posterior, save_tcri_session, real TCRIModel with n_latent=128) and the fabricated names (global_joint_distribution, get_clones) are gone from the output.

Notes / follow-ups

• Structure only; per the roadmap, D1 (writing the docstrings) layers underneath — :undoc-members: currently surfaces functions without descriptions.
• The public surface still includes internal-looking helpers and *_tl aliases; trimming that is API cleanup (chore: remove committed junk files (#26) #16/build: migrate setup.py → pyproject.toml (PEP 621) (#21) #17), and these pages will track it automatically.
• RTD builds on Python 3.9 with an unpinned sphinx>=4.0.0 (D6 territory) — not touched here.

Closes Notion D11.

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