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Garlic SynCom6 graph: remove design-workflow nodes and bound the radish seedling endpoint #1476

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@realmarcin

CommunityMech:000095; Garlic_Pseudomonas_SynCom6; PMID:32762153; doi:10.1111/1751-7915.13640.

The complete cached primary main body/Methods/captions separates field Pseudomonas enrichment/co-occurrence screening in garlic from equal-proportion SynCom construction and the two-day radish seedling-length assay. Selection and assembly are experimental workflow, not ecological interactions. The earlier 2026-10-02 curation removed both workflow arrows but left these two nodes. The M and M+B groups outperform sterile-water CK and B8-7 alone; B8-7 neither promotes radish growth nor significantly changes M's effect. The experiment does not compare M against each of its six Pseudomonas monocultures and cannot assign six-strain synergy, each strain's necessity, field garlic yield benefit or a metabolite mechanism.

Acceptance: remove the two workflow nodes and their unsupported GO symbiosis annotations; preserve a single bounded community-level radish growth outcome with explicit in-vivo evidence and canonical Pseudomonas umbrella participant. Do not invent six species IDs from provisional 16S names. Preserve the prior arrow-removal event and all non-graph raw blocks; document screening/assembly context and the unresolved mechanism/roster in a discussion. Add guarded history, focused tests, regenerated page and review/validation records. No new causal structure or provider spend required.

Source-based self-adversarial review, not independent approval. All three whole YAML records were read. Main text, Methods and embedded captions were read; no figure images, separate supplementary files, raw data or analysis code audited. Dedup searched 790 all-state issue titles/bodies and ignored/hidden-inclusive reports, research, history, tests, scripts and workflows. Five matched issue bodies (#624/#543/#486/#326/#17) and the UFMP/Garlic prior history artifacts were read; none duplicates these source-specific causal-scope repairs. Existing validation and render logs also match record names but do not constitute completed source reviews. Not every issue comment or PR review was inspected.

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  1. realmarcin commented on Oct 6, 2026

    @realmarcin
    ContributorAuthor

    Addressed in #1477 at 7bdc938; exact-head self-adversarial review: #1477 (review). 451 passed in 209.31s (0:03:29); post-commit docs-current passed. Decisions, actual outputs and limitations are committed. Zero graph errors; 33 prior warnings plus one explicit SPH2 coverage warning. Not independent approval. Close only after protected main merge.

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