refactor(seqopt): make SeqOpt core (lazy ShapModel); only mode='impact' needs pro

[breimanntools]

Summary

Make SeqOpt a core class — only the SHAP-guided mode="impact" needs aaanalysis[pro].

The EA machinery (NSGA-II, all operators), SeqOptPlot, and mode="importance" are pure-Python and need nothing pro; only mode="impact" uses SHAP. So:

• Lazy ShapModel import inside the impact path → SeqOpt is importable in a base install. Constructing mode="impact" without shap raises a friendly aaanalysis[pro] install hint.
• Moved SeqOpt/SeqOptPlot + _backend/seqopt/ from protein_design_pro/ into the core protein_design/ subpackage; removed the now-empty protein_design_pro package.
• __init__.py: pro try/except gate → core exports of SeqOpt/SeqOptPlot.
• Updated: DEDICATED_OWNERS, test imports (+ tests dir → seqopt_tests, shap-guard only the impact tests), the comparison script, the [pro] markers, ADR-0043 (D1 amended), CONTEXT.md, the release note, and the docstring-guide table — all to "core; mode="impact" needs pro".

Verification

Verified with shap blocked (simulated base install): import works, mode="importance" runs, mode="impact" raises the pro hint — with a regression test. 96 SeqOpt tests + 268 in the broad gate; docstrings 0 defects; merged current with master.

(Why: the convention test test_docstring_contracts requires every *_pro symbol to be [pro], so a core class can't live in a _pro package — hence the move.)

🤖 Generated with Claude Code

[breimanntools]

This looks fine

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 96.13%. Comparing base (ae64fe2) to head (2a6a6f5).
⚠️ Report is 3 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #279      +/-   ##
==========================================
- Coverage   96.13%   96.13%   -0.01%     
==========================================
  Files         176      175       -1     
  Lines       16827    16823       -4     
  Branches     2877     2877              
==========================================
- Hits        16176    16172       -4     
  Misses        366      366              
  Partials      285      285              

Files with missing lines	Coverage Δ
aaanalysis/__init__.py	97.01% <100.00%> (-0.32%)	⬇️
aaanalysis/protein_design/__init__.py	100.00% <100.00%> (ø)
...aanalysis/protein_design/_backend/seqopt/genome.py	82.60% <ø> (ø)
...analysis/protein_design/_backend/seqopt/metrics.py	89.74% <ø> (ø)
aaanalysis/protein_design/_backend/seqopt/nsga2.py	95.53% <ø> (ø)
...analysis/protein_design/_backend/seqopt/penalty.py	92.85% <ø> (ø)
aaanalysis/protein_design/_backend/seqopt/run.py	94.02% <ø> (ø)
aaanalysis/protein_design/_seqopt.py	89.07% <100.00%> (ø)
aaanalysis/protein_design/_seqopt_plot.py	92.04% <ø> (ø)

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

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