docs: TMD means Target Middle Domain, and it is already the abstraction

[breimanntools]

The published Feature Identification chapter has always said Target Middle Domain (TMD). The glossaries had drifted away from it.

CONTEXT.md called the part vocabulary "TMD-centric" and "semantically wrong" for non-domain levels, and told the reader to "replace the generic tmd with the specific domain name". docs/source/index/glossary.rst said the same.

Read literally, that describes a defect — so it kept generating proposals to add a region-naming layer to CPP. Three independent planning passes (a codex planner, a subagent, and this session) each reached that conclusion from the text alone, and each designed a region= parameter, a rename mapping, and somewhere to store it. The maintainer stopped it before a line was written.

There is nothing to rename. The vocabulary is a geometry: one target middle domain flanked by two juxta middle domains, applying unchanged to a Pfam domain, a cleavage-site window or a whole chain. A feature id reading TMD-Segment(2,4)-ANDN920101 does not assert a transmembrane helix.

Stated in six places, all pointing at one canon

file	what it now says
usage_principles/feature_identification.rst	the canon — an important admonition and the part_vocabulary anchor (plus a JMD-C typo fix: it read "N-terminal")
glossary.rst	the part and df_parts entries, cross-referencing the anchor
CONTEXT.md	the part entry, and a note that it had drifted from the published chapter
_schemas.py	the df_parts description, rendered into the schema page
_constants.py	the comment above DICT_PART_LABEL, replacing the stale "reserved for the #27 region abstraction" note
CLAUDE.md	an always-loaded rule, so an agent reads it before designing

Comment and description strings only in the two Python files — no code changed, CPP untouched. df_schemas.rst is regenerated from the edited schema so its sync test passes (341 API tests green).

🤖 Generated with Claude Code

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 95.39%. Comparing base (3c11c90) to head (9b090d6).

Additional details and impacted files

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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           

Files with missing lines	Coverage Δ
aaanalysis/_constants.py	100.00% <ø> (ø)
aaanalysis/_schemas.py	96.62% <ø> (ø)

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

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