ORT graph: expose gapfilled nitrogen-gas production and modeled substrate coupling #1525

Record:KBase_ORT_Workflow_Community_Model.yaml (000038),3 nodes/2 arrows; https://doi.org/10.1093/bioinformatics/btab753.

Neither Steroidobacteraceae MAG encoded nitrogen-gas production: N2O-to-N2 was added by gapfilling. Preserve this modeled output, not demonstrated genome-supported field metabolism. Retain sequential nitrate supply and carbon-linked stoichiometry as model-bounded PARTIAL routes; no obligatory reciprocal syntrophy, exclusive upstream nitrate source, traced carbon transfer or experimentally identified field limiting factor. Use explicit canonical nitrifier and denitrifier subsets, retaining the two distinct denitrifier names despite shared family CURIE. Carbon15-23 applies to site models, not automatically each denitrifier. Replace narrative concentration fields with contextual notes within the graph. Iterative coupling was not demonstrated in this single-input proof of concept.

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Dedup:827 all-state issue titles/bodies, broader synonyms,38 ignored/hidden local matches and relevant source/history/test contexts; not every comment/PR. Whole records reviewed. Self-adversarial review is not independent approval. Keep repair issues open until protected-main merge; metadata/provenance followups remain open until separately resolved.