NEXT_TASKS: reconcile to 2026-07-29 - #263
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…thread) Reconciled against merged PRs since the stale 2026-07-21 date. Marked DONE: - 000031 re-scoping (#256) — was "curator decision still open"; resolved by PR #262. Added a dedicated section recording what changed and why it was a defect rather than a controversy. - Li et al. 2024 ingestion (#259) — was "still not ingested"; PR #261 cached it via the new --from-file path and curated 000068. - §2 "apply modeled_environment matching to the ingredient suggester" — this was never actually pending: suggest_related_ingredients.py has read modeled_environment since PR #220 that created it. §2/#30 now has no actionable remainder here. Corrected a wrong claim that was sitting in the file: the Li 2024 summary said "5-10 mM promotes, >=30 mM inhibits". The >=30 mM part came from the Edison report and describes the paper's anaerobic-sludge system; in the coculture the response is non-monotonic (30 mM recovers in the later stage, only 50 mM inhibits). Also noted that one quoted snippet from that report appears nowhere in the paper. Newly logged: PR #255 (Suillus-Bacillus thiamine SynCom) has been open since 2026-07-26, non-draft, MERGEABLE/CLEAN with all gates green, and was absent from this file entirely. Still open and unchanged: #257 (validate-references reporting), #258 (14 dangling edges, triage), #259 (automated retrieval from blocking publishers), and the upstream-blocked term-minting items in sections 0/1. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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Routine backlog reconciliation — doc-only.
Reconciled
NEXT_TASKS.mdagainst merged PRs since its staleLast reconciled: 2026-07-21.Marked DONE
--from-filepath and curated 000068.modeled_environment— never actually pending.suggest_related_ingredients.pyhas readmodeled_environmentsince PR Finalize CHEBI-route ingredient suggester (MediaIngredientMech#119) #220, the PR that created it. §2 / issue Enhance cross-repository environmental linking with CultureMech and MediaIngredientMech #30 now has no actionable remainder in this repo.Corrected a wrong claim already in the file
The Li 2024 summary read "5–10 mM promotes, ≥30 mM inhibits". The ≥30 mM half came from the Edison report and describes the paper's anaerobic-sludge system; in the coculture the response is non-monotonic — 30 mM "was improved instead of inhibited in the later stage", only 50 mM inhibits. Also recorded that one snippet quoted by that report appears nowhere in the paper.
Newly logged
PR #255 (Suillus-Bacillus thiamine SynCom) has been open since 2026-07-26 — non-draft, MERGEABLE/CLEAN, all gates green — and was absent from this file entirely.
Unchanged / still open
#257, #258 (triage), #259 (automated retrieval from blocking publishers), and the upstream-blocked term-minting items in §0/§1.
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