doc(use-cases): add Use Cases guide + UC1 γ-secretase reproduction

[breimanntools]

What

Introduces Use Cases as a third subchapter under the GUIDES nav (alongside Tutorials and Protocols) and ships the first one. A use case reproduces a published study end to end from bundled data only — distinct from Tutorials (one tool) and Protocols (one minimal-code workflow).

Note on nav placement: issue #109's original text says "Examples umbrella caption", but the live nav uses the GUIDES caption (Tutorials · Protocols), so per direction this lands as GUIDES → Use Cases. Same use_cases/ folder + create_notebooks_docs.py wiring the issue specifies.

First use case — use_case1_gamma_secretase.ipynb

Reproduces the key results of Breimann et al., Charting γ-secretase substrates by explainable AI, Nat. Commun. 16, 5428 (2025) — the paper AAanalysis was built to support — on the bundled, balanced DOM_GSEC set (63 substrates + 63 non-substrates), no downloads:

• CPP signature — feature map + profile (cf. Fig 2b/2c), concentrated in the TMD_C_JMD_C cleavage region, Conformation dominant (matches the paper's biology).
• Benchmark (cf. Fig 3a) — CPP 84.9% vs scale-average baseline 75.4% balanced accuracy (5-fold CV, same tree model). Matches the paper's 84% headline; the narrower baseline gap vs the paper's ~50% is expected on this balanced, proteome-free set and is called out in the notebook.
• Simplifications documented in-notebook: balanced bundled set (not the imbalanced proteome), one tree ensemble (not the 10-model LOO sweep), single bundled TMD annotation (not the UniProt/TMHMM/Phobius comparison). Scaling up = the Protocols.

Wiring

• export_use_case_notebooks_to_rst() in create_notebooks_docs.py + call in conf.py
• new docs/source/use_cases.rst toctree; added to the GUIDES caption in index.rst
• landing-page routing line updated (was "coming soon") + release note

Local gates

• pytest --nbmake on the notebook: 1 passed
• cd docs && make html: use_cases.html + RST + 3 figures render, zero net-new Sphinx warnings

Scope

Docs-only; no public API change. Advances #109 (does not close it — the first milestone also wants one case per prediction level; this delivers the infrastructure + the γ-secretase flagship). Part of epic #106.

[breimanntools]

Not sure how good the notebook will be. I check it after it is pusehd

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 96.16%. Comparing base (ae64fe2) to head (b1764dc).
⚠️ Report is 3 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #277      +/-   ##
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+ Coverage   96.13%   96.16%   +0.03%     
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  Files         176      176              
  Lines       16827    16856      +29     
  Branches     2877     2882       +5     
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+ Hits        16176    16210      +34     
+ Misses        366      359       -7     
- Partials      285      287       +2     

see 3 files with indirect coverage changes

Components	Coverage Δ
cpp_core	94.95% <ø> (ø)

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