fix(hsj): translate token indices to state indices in HSJ scoring (T-375, T-376) - #280

Merged

ms609 merged 11 commits into

feature/hsj-token-index-fix

Aug 2, 2026

Commits on Aug 1, 2026

fix(hsj): translate token indices to state indices before comparison (T-375, T-376)
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test(hsj): add regression coverage that permutes contrast rows, not levels (T-375, T-376)
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docs: regenerate MaximizeParsimony.Rd (roxygen sync, pre-existing drift)
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docs(hsj-paper-oracle): caveat that check [3] passing here isn't a T-374 fix
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test(hsj): add a value-level T-375 regression test (secondary "?" resolution invariant)
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fix(ts_hsj_score): validate tip_labels/absent_state bounds
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docs: promote T-374 caveat to printed output; log HSJ scoring change in NEWS
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fix(hsj): validate tip_labels/absent_state on the production search path too
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perf(hsj): restore per-character tie-break array sizing, reuse ctz64()
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docs(hsj): fix review-flagged doc gaps -- NEWS accuracy, stale terminology, vignette
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fix(news): reword to avoid an unlisted possessive-acronym spelling flag
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