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Remove inference and subset-comparison arrows from Parmigiano set2 graph #1678

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@realmarcin

CommunityMech:000431; PMID41859451. Preserve four biological assay nodes, positive St/Ld pair versus both monocultures, lower Lh/Ld pair rates, highest triculture total lactate and set2 St/Ld rate comparable to triculture. Remove acidification-to-inferred-C5I3-activity arrow and pair-to-triculture comparison arrow: neither is a demonstrated causal process. Rename D-lactate node to the measured triculture pool, not a specific producer; Lh and St can also contribute D-lactate. Preserve #1077-1079 fixes and existing molecular mechanism gap. Close only after protected-main merge.

Searched 954 all-state issue titles/bodies; read all five matches (#1077-1079, #497, #258), the previous milk review, and the existing Polaromonas author-request lead. Local hidden/ignored-inclusive search found 64 matching files, excluding .git/docs/site/references_cache. Four whole records and four fresh complete primary main texts/captions read; seven further abstracts checked. No original figure pixels or separate supplements audited. Self-adversarial review, not independent approval.

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  1. realmarcin commented on Oct 7, 2026

    @realmarcin
    ContributorAuthor

    Addressed in #1684 at 72da5ae; exact-head self-review:#1684 (review). 736 passed in 494.44s (0:08:14); post-commit docs-current passed. Every-node/every-arrow decisions and actual output digests committed. Not independent approval; close only after protected-main merge. Metadata #1683 remains unfinished; all four current reference gates passed.

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