docs: record that TMD was Transmembrane Domain before it was Target Middle Domain

[breimanntools]

The wording added earlier said TMD means Target Middle Domain "not transmembrane domain". That flattens a design decision into a correction — and it is wrong in the one place it matters most: in the γ-secretase work the span really is the transmembrane domain.

The history is the explanation. CPP was first applied to γ-secretase substrates, where the span of interest is the transmembrane domain and its flanks are the juxtamembrane domains. When the method was generalized beyond membrane proteins the acronyms were deliberately kept and re-read — TMD as Target Middle Domain, JMD as Juxta Middle Domain. Same letters, same geometry, wider meaning, nothing to rename per data set.

Stated in the three places a reader meets it:

• the Feature Identification chapter, whose admonition now leads with the origin and says a feature id describes a transmembrane helix only when the data are membrane proteins, as in the case study below it
• the part entry in CONTEXT.md, the internal glossary whose earlier wording generated the region-renaming proposals in the first place
• the γ-secretase use case, right where the reader meets jmd_n / tmd / jmd_c, since that analysis is the one the vocabulary is named after and the literal reading is the correct one there

Documentation only. The notebook change is a markdown cell, so its executed outputs are untouched. Docs gate: 0 errors, critical at baseline (167).

Context: #27 was closed on this basis.

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 95.39%. Comparing base (fc8e21e) to head (3daa4cf).

Additional details and impacted files

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##           master     #591   +/-   ##
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  Coverage   95.39%   95.39%           
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  Files         222      222           
  Lines       23387    23387           
  Branches     4073     4073           
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  Hits        22309    22309           
  Misses        631      631           
  Partials      447      447           

Components	Coverage Δ
cpp_core	95.97% <ø> (ø)

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