fix(cpp): make CPP splits usable on free peptides with no flanks (#338)

[breimanntools]

Closes #338.

Summary

Pattern/PeriodicPattern splits and aap.find_features were unusable on free peptides with no
flanking context (the linear-epitope case): the default split config requires each part to be >= 15
residues, so any target region shorter than ~15 aa raised an opaque "too short" ValueError.

Details

• Actionable error: check_match_df_parts_split_kws now names the binding split length (which
  split type / parameter drives n_max) and the concrete fix (Segment-only splits, lower
  len_max/n_split_max, or add jmd_n/jmd_c context).
• Honor kws: find_features kws now accepts len_max and actually threads
  n_split_max/len_max into the split config for the fast path (previously ignored) and the
  CPPGrid search stages.
• Auto-fit (fast path): the split config auto-fits to the shortest part, dropping
  Pattern/PeriodicPattern and clamping n_split_max with a single UserWarning, so free peptides
  run out of the box. Byte-identical when parts are long enough.
• Search Stage 3: the simplify CPP now uses the winner's split_kws instead of the default,
  which previously hard-errored on short parts even though the grid had gracefully soft-dropped the
  non-fitting configs.

Results for flanked inputs are unchanged (byte-identical), proven by a fast-path A/B hash comparison
master-vs-branch.

Ripple

• unit tests: actionable message, Segment-only / reduced-len_max short-part paths, the auto-fit
  helper (drop/clamp + warning), and free-peptide fast/balanced runs.
• release-notes Unreleased Fixed entry, placed in the Version 1.1 section (consolidates with CPP.run(n_jobs>1) crashes with multiprocessing.Manager() EOFError outside notebooks #339's
  Fixed entry on merge).

Part of epic #336.

🤖 Generated with Claude Code

[codecov]

Codecov Report

❌ Patch coverage is 87.75510% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 94.83%. Comparing base (7dcc8d8) to head (b755e5c).
⚠️ Report is 6 commits behind head on master.

Files with missing lines	Patch %	Lines
aaanalysis/pipe/_find_features.py	83.87%	4 Missing and 1 partial ⚠️
...ysis/feature_engineering/_backend/check_feature.py	94.44%	0 Missing and 1 partial ⚠️

❌ Your patch check has failed because the patch coverage (87.75%) is below the target coverage (90.00%). You can increase the patch coverage or adjust the target coverage.

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #349   +/-   ##
=======================================
  Coverage   94.83%   94.83%           
=======================================
  Files         196      196           
  Lines       18767    18794   +27     
  Branches     3175     3180    +5     
=======================================
+ Hits        17797    17823   +26     
- Misses        633      634    +1     
  Partials      337      337           

Files with missing lines	Coverage Δ
...ysis/feature_engineering/_backend/check_feature.py	93.43% <94.44%> (ø)
aaanalysis/pipe/_find_features.py	58.11% <83.87%> (+3.66%)	⬆️

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

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