Bound infant gut persistence and prebiotic causal claims (batch54)

[realmarcin]

Scope

Closes #1511. Closes #1512. Closes #1513.
Related #1514 and #1515 remain OPEN: exact SynCom membership/missing structure and E. coli-specific persistence representation are unresolved.

• Bound phage persistence to strain-resolved associations and partial maternal/recoding mechanisms.
• Preserve SynCom omission and acid-challenge results without direct-transfer or universal pH claims.
• Correct persistence trait ownership and preserve taxon-specific genomic associations.

Adversarial Review

• Whole219-line phage,209-line prebiotic and250-line maternal bacterial records read, including all10 original nodes and7 arrows. Complete primary main texts/Methods and main captions/tables read for all3 sources. No original figure pixels, external supplements, raw data or code audited. The prebiotic paper is version1 of a preprint, not peer reviewed.
• Phage155/1801 persistence denominator refers to40 eligible infants, not every maternally shared or Bacteroides-associated phage. Maternal/Bacteroides canonical entries represent a subset. Predicted host/lifestyle and sharing are not universal lytic predation or an isolated maternal-transfer experiment.
• Recoding persistence association remains positive. Three early recoded persisters have heterogeneous TAG trajectories including decreases; no universal increase or selectively demonstrated delayed-lysis effect. Community richness differs from within-phage nucleotide diversity; richness-to-persistence arrow removed.
• Phage population ANI99 percent/75 percent compared sequence is distinct from bacterial99.999 percent/50 percent. Coverage and CRISPR correlations do not prove continuous infection of an unchanged host lineage. Both retained phage arrows are PARTIAL with actual proposed mechanisms.
• SynCom has six species and differs from donor-derived communities containing P. dorei/L. rhamnosus. Four canonical entries are an explicitly cross-experiment subset, not an exact four-member experiment. Roster/strain identifiers and missing R. gnavus structure remain1514; no guessed CURIE or invented member added.
• Positive omission/Raman-FISH result is higher E. coli metabolic activity with P. vulgatus PRESENT underGOS; direction verified against primary Results and a short exact excerpt. An interim continuation summary inverted this direction, caught before any record edit. Source notes, issues and final records have the correct direction. Abundance invariance belongs to this assay, not every substrate experiment.
• Succinate/propionate output is not demonstrated direct transfer to E. coli. Conditioned supernatants did not reproduce the GOS/glucose growth difference. Retain community intervention evidence with SUPPORT; remove the overview-to-component arrow, not the controlled result.
• Lactate-versus-acetate challenge supports species-dependent inhibition, while the main text discusses additive pH/acid effects. Exact challenge protocol is absent from inspected main Methods; no claim that an uninspected supplement lacks it, and no invented pH-clamped control. Fermentation-to-inhibition remains PARTIAL pending selective depletion/rescue.
• Bifidobacterium12 persisters/18 non-persisters CAZyme genomic association retained as positive computational evidence. E. coli3/25 iron, adhesion and toxin annotations are not transferred to Bacteroides/Bifidobacterium. Missing E. coli representation remains1515, with positive findings explicitly retained in discussion.
• Bacterial59/560 denominator and month8-or-later endpoint are explicit; maternal-sharing association is not a dominant cause applying uniformly to Bifidobacterium. Clinical/prematurity/antibiotic/feeding confounding remains explicit. Non-graph descriptions and taxonomy are preserved, not certified.
• Future ex-vivo motility structure must preserve negative controls: full and P. vulgatus-omitted supernatants both suppress mouse-colon motility, matching SCFAs do not reproduce it, and endogenous PEA was below detection. No infant in-vivo physiology or established endogenous PEA mediator is asserted.
• Full record diffs, all8 focused tests, participant-registry and cache diff inspected.10 nodes retained;2 arrows removed;5 PARTIAL arrows remain. Only graph/discussion/curation-history record fields change;457 other records and raw non-graph blocks unchanged.919 caches unchanged; one exact-prefix appendix adds16 XML-verified source words with attribution and digest.
• Actual focused schema/strict/term/reference/snippet/history/rank gates passed. All34 baseline network findings preserved with zero structural errors. Repeat render deterministic and exact descriptions parser-checked over456 pages, not browser screenshots. Two source-backed pairwise-to-community corrections yield measured mixed125, community-only264 and1226 solely community-credited taxa; no production matching or census-bound change.
• Dedup searched817 all-state issue titles/bodies and43 ignored/hidden local files; relevant contexts inspected, not every historical comment/review.1511-1513 addressed but open until protected main merge;1514-1515 unresolved. Two separate Edison dry runs only, no provider call or spend. Self-adversarial review is not independent approval.

Verification And Output Records

511 passed in 220.50s (0:03:40); eight new focused tests. Actual schema, strict, term, reference, snippet and history gates pass. 28 snippets match selected caches. Text matching is not independent source provenance or scientific support. One cache gains16 primary-verified words with XML digest and original exact prefix;919 other caches unchanged. CLI Total checks counts reported issues, not executed checks. SupportingReference coverage476, Linux DOI-cache lookup1091 and selected-cache provenance1362 remain limitations.

All10 nodes retained, two unsupported arrows removed, five explicitly PARTIAL mechanisms retained. Positive omission and acid-challenge findings remain SUPPORT; E. coli activity is higher with P. vulgatus present underGOS. Bacterial iron/adhesion ownership is not transferred from E. coli to other genera. Both-root baseline retained; zero structural errors and all34 prior network findings unchanged. All457 other records and raw non-graph blocks preserved, not certified. Measured census: mixed125, community-only264, solely community-credited taxa1226; no production matching or census-bound change.

Repeat renders deterministic; exact descriptions parser-checked across456 pages, not browser screenshots. Actual post-commit just check-docs-current exited0 with clean tree; log SHA256 389133b2c7e4d416748aaac80512b9dc8559a1dc529d2e4c10e7d40a61385bb9.

Every-node/every-arrow decisions, actual output digests and self-adversarial review committed under reports/causal_graph_review, batch54. Not independent approval. Corpus184 reviewed /258 pending /18 needs_research, not complete.

Dependency

Draft depends on #1510. Do not merge into the topic parent. Require eligible exact-head CI and the protected main queue after parent merges. Move dependents before deleting merged branches. Two separate one-community Edison dry runs only, no provider job or spend; full-prompt review, specific payload/spend authorization and primary-checked report review remain prerequisites to new structure.

[realmarcin]

Source-based self-adversarial review at exact head e2dacf7; not independent approval.

Repairs #1511, #1512 and #1513 addressed; #1514 and #1515 remain unresolved.

• Bound phage persistence to strain-resolved associations and partial maternal/recoding mechanisms.

• Preserve SynCom omission and acid-challenge results without direct-transfer or universal pH claims.

• Correct persistence trait ownership and preserve taxon-specific genomic associations.

• Whole219-line phage,209-line prebiotic and250-line maternal bacterial records read, including all10 original nodes and7 arrows. Complete primary main texts/Methods and main captions/tables read for all3 sources. No original figure pixels, external supplements, raw data or code audited. The prebiotic paper is version1 of a preprint, not peer reviewed.

• Phage155/1801 persistence denominator refers to40 eligible infants, not every maternally shared or Bacteroides-associated phage. Maternal/Bacteroides canonical entries represent a subset. Predicted host/lifestyle and sharing are not universal lytic predation or an isolated maternal-transfer experiment.

• Recoding persistence association remains positive. Three early recoded persisters have heterogeneous TAG trajectories including decreases; no universal increase or selectively demonstrated delayed-lysis effect. Community richness differs from within-phage nucleotide diversity; richness-to-persistence arrow removed.

• Phage population ANI99 percent/75 percent compared sequence is distinct from bacterial99.999 percent/50 percent. Coverage and CRISPR correlations do not prove continuous infection of an unchanged host lineage. Both retained phage arrows are PARTIAL with actual proposed mechanisms.

• SynCom has six species and differs from donor-derived communities containing P. dorei/L. rhamnosus. Four canonical entries are an explicitly cross-experiment subset, not an exact four-member experiment. Roster/strain identifiers and missing R. gnavus structure remain1514; no guessed CURIE or invented member added.

• Positive omission/Raman-FISH result is higher E. coli metabolic activity with P. vulgatus PRESENT underGOS; direction verified against primary Results and a short exact excerpt. An interim continuation summary inverted this direction, caught before any record edit. Source notes, issues and final records have the correct direction. Abundance invariance belongs to this assay, not every substrate experiment.

• Succinate/propionate output is not demonstrated direct transfer to E. coli. Conditioned supernatants did not reproduce the GOS/glucose growth difference. Retain community intervention evidence with SUPPORT; remove the overview-to-component arrow, not the controlled result.

• Lactate-versus-acetate challenge supports species-dependent inhibition, while the main text discusses additive pH/acid effects. Exact challenge protocol is absent from inspected main Methods; no claim that an uninspected supplement lacks it, and no invented pH-clamped control. Fermentation-to-inhibition remains PARTIAL pending selective depletion/rescue.

• Bifidobacterium12 persisters/18 non-persisters CAZyme genomic association retained as positive computational evidence. E. coli3/25 iron, adhesion and toxin annotations are not transferred to Bacteroides/Bifidobacterium. Missing E. coli representation remains1515, with positive findings explicitly retained in discussion.

• Bacterial59/560 denominator and month8-or-later endpoint are explicit; maternal-sharing association is not a dominant cause applying uniformly to Bifidobacterium. Clinical/prematurity/antibiotic/feeding confounding remains explicit. Non-graph descriptions and taxonomy are preserved, not certified.

• Future ex-vivo motility structure must preserve negative controls: full and P. vulgatus-omitted supernatants both suppress mouse-colon motility, matching SCFAs do not reproduce it, and endogenous PEA was below detection. No infant in-vivo physiology or established endogenous PEA mediator is asserted.

• Full record diffs, all8 focused tests, participant-registry and cache diff inspected.10 nodes retained;2 arrows removed;5 PARTIAL arrows remain. Only graph/discussion/curation-history record fields change;457 other records and raw non-graph blocks unchanged.919 caches unchanged; one exact-prefix appendix adds16 XML-verified source words with attribution and digest.

• Actual focused schema/strict/term/reference/snippet/history/rank gates passed. All34 baseline network findings preserved with zero structural errors. Repeat render deterministic and exact descriptions parser-checked over456 pages, not browser screenshots. Two source-backed pairwise-to-community corrections yield measured mixed125, community-only264 and1226 solely community-credited taxa; no production matching or census-bound change.

• Dedup searched817 all-state issue titles/bodies and43 ignored/hidden local files; relevant contexts inspected, not every historical comment/review.1511-1513 addressed but open until protected main merge;1514-1515 unresolved. Two separate Edison dry runs only, no provider call or spend. Self-adversarial review is not independent approval.

511 passed in 220.50s (0:03:40); eight new focused tests. Actual schema, strict, term, reference, snippet and history gates pass. 28 snippets match selected caches. Text matching is not independent source provenance or scientific support. One cache gains16 primary-verified words with XML digest and original exact prefix;919 other caches unchanged. CLI Total checks counts reported issues, not executed checks. SupportingReference coverage476, Linux DOI-cache lookup1091 and selected-cache provenance1362 remain limitations.

All10 nodes retained, two unsupported arrows removed, five explicitly PARTIAL mechanisms retained. Positive omission and acid-challenge findings remain SUPPORT; E. coli activity is higher with P. vulgatus present underGOS. Bacterial iron/adhesion ownership is not transferred from E. coli to other genera. Both-root baseline retained; zero structural errors and all34 prior network findings unchanged. All457 other records and raw non-graph blocks preserved, not certified. Measured census: mixed125, community-only264, solely community-credited taxa1226; no production matching or census-bound change.

Repeat renders deterministic; exact descriptions parser-checked across456 pages, not browser screenshots. Actual post-commit just check-docs-current exited0 with clean tree; log SHA256 389133b2c7e4d416748aaac80512b9dc8559a1dc529d2e4c10e7d40a61385bb9.

Every-node/every-arrow decisions, actual output digests and self-adversarial review committed under reports/causal_graph_review, batch54. Not independent approval. Corpus184 reviewed /258 pending /18 needs_research, not complete.

Protected main merge remains pending.

[github-actions]

Network integrity findings

Warnings only — a member with no interaction yet, or a participant matched by ontology id rather than by name, or one on a community-level interaction that resolves to no member. Reported, but does not fail the build.

Network Integrity Audit Report
================================================================================

0 error, 34 warning across 14 records with findings
Only error-severity findings fail the build.

Algal_Methanotroph_Biogas_Valorization_Coculture
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Leptolyngbya' has no interactions

Total: 1 issues (0 error, 1 warning)

At_RSPHERE_SynCom
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Flavobacterium sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Rhodococcus sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Streptomyces sp.' has no interactions
  [warning] DISCONNECTED: Taxon 'Variovorax sp.' has no interactions

Total: 5 issues (0 error, 5 warning)

Australian_Lead_Zinc_Polymetallic
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Acidithiobacillus ferrooxidans' has no interactions
  [warning] DISCONNECTED: Taxon 'Leptospirillum ferriphilum' has no interactions

Total: 2 issues (0 error, 2 warning)

Bacillus_G12_Y4_X25_Tobacco_Biocontrol_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'tobacco' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'tobacco' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Bacillus_siamensis_vallismortis_HT_Masson_Pine_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'Fusarium oxysporum' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Pinus massoniana' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Pinus massoniana' not found in taxonomy section (community-level scope)

Total: 3 issues (0 error, 3 warning)

Brocadia_Low_Nitrogen_Anammox_Consortium
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Ca. Kuenenia early-acclimation lineage' has no interactions

Total: 1 issues (0 error, 1 warning)

Dangl_SynComm_35
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Escherichia coli DH5α' has no interactions
  [warning] DISCONNECTED: Taxon 'Flavobacterium species' has no interactions
  [warning] DISCONNECTED: Taxon 'Microbacterium species' has no interactions
  [warning] DISCONNECTED: Taxon 'Stenotrophomonas species' has no interactions
  [warning] DISCONNECTED: Taxon 'Xanthomonadales members' has no interactions

Total: 5 issues (0 error, 5 warning)

Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Methylophaga' has no interactions

Total: 1 issues (0 error, 1 warning)

East_River_Floodplain_Core_Microbiome
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Acidobacteriota floodplain representatives' has no interactions
  [warning] DISCONNECTED: Taxon 'Nitrospirae core floodplain members' has no interactions

Total: 2 issues (0 error, 2 warning)

GLBRC_UFMP_Fermentation_Community
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'RUG023 sp. (MAG SPH2)' has no interactions

Total: 1 issues (0 error, 1 warning)

Mangrove_Benzene_MFC_Bioanode_Consortium
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Pelobacter' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas' has no interactions

Total: 2 issues (0 error, 2 warning)

Nitrifying_Wastewater_Ammonia_Oxidizing_Consortium
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Legionella MAGs' has no interactions

Total: 1 issues (0 error, 1 warning)

Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Space_Habitat_SevenMember_Stress_Tolerance_SynCom
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Acinetobacter radioresistens 50V1' has no interactions
  [warning] DISCONNECTED: Taxon 'Micrococcus luteus W4-Al-K1' has no interactions
  [warning] DISCONNECTED: Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas antarctica CMS 35T' has no interactions
  [warning] DISCONNECTED: Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions
  [warning] DISCONNECTED: Taxon 'Streptococcus halotolerans HTS9T' has no interactions

Total: 6 issues (0 error, 6 warning)

The full report is attached to the workflow run as an artifact.

[realmarcin]

Self-adversarial review refreshed at exact head 026e85687f8f5a3dfb4b3c26d51b04461691c418
after protected main merge of #1350. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 734a4ea137b8f273578794858d8ca9cd34e08ba1.
The batch-owned binary patch is byte-identical
(SHA-256 9aacaf4e78b7da4f2e1a13078691167aa72cf651f2546b1eed44f80c7821bba1); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial review refreshed at exact head 0624ac181ce8abb56923a130ebb6e759411004db
after protected main merge of #1355. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 734a4ea137b8f273578794858d8ca9cd34e08ba1.
The batch-owned binary patch is byte-identical
(SHA-256 9aacaf4e78b7da4f2e1a13078691167aa72cf651f2546b1eed44f80c7821bba1); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial integration review at exact head fcdccf614e2df57f0c1052ee622703b18ec55328. Not independent approval.

Integrated already-merged schema prerequisite #1692 (67603e192525899fae75420e2c19e8212b16afc9). Compared with the prior reviewed head 0624ac181ce8abb56923a130ebb6e759411004db, the only changes are the canonical schema pin, shared schema and generated datamodel from that main commit. Every other tracked file is identical; the batch-owned binary patch remains byte-identical (SHA-256 9aacaf4e78b7da4f2e1a13078691167aa72cf651f2546b1eed44f80c7821bba1). All 60 published batch patches were checked this way. No scientific assertion, reference cache, history, decision ledger or generated page was edited by this integration.

Adversarial checks: no inherited schema-file edits lost; generated CrossCorpusLink remains standalone and does not add a causal claim; normal strict validation passed all 460 records; required CrossCorpusLink fields enforced. Fresh broad regression runs on both ends of the stack: 302 passed in 172.77s (0:02:52); 756 passed in 255.55s (0:04:15). Docs-current passed clean at batches25/84, and vendored-sync passed. The 58 intermediate combinations were not independently retested. Existing primary-source review limitations and unresolved research issues remain applicable; historic validation receipts are not rewritten as new scientific reviews.

An additional generated-datamodel loading check FAILED and is retained in the integration receipt. Differential testing found exactly the same failures on all 460 paths before and after this integration:417 unhashable TaxonDescriptor and43 unhashable CultureCollectionEnum exceptions, with linkml-runtime1.11.1. Existing tests explicitly use plain YAML instead of this loader. Pre-existing defect #1703 remains OPEN; no datamodel-loader success is claimed. Normal strict schema validation is a separate passing path, not a relabeling of that failure.

Required CI must pass on this exact head and the protected merge-queue candidate. No manual workflow dispatch, artificial status, administrative merge or protection bypass. Dependents stay draft until their parent is confirmed merged; move dependents before branch deletion.

[realmarcin]

Self-adversarial review refreshed at exact head 725ec42223a8ea31e3bc7464731a1f22574d2b4c
after protected main merge of #1361. This is not independent approval.

The entire tree remains identical to the preceding reviewed tree 0b333ae51e7dcc1add0ded6d0fd6e5245b8cde6a.
The batch-owned binary patch is byte-identical
(SHA-256 9aacaf4e78b7da4f2e1a13078691167aa72cf651f2546b1eed44f80c7821bba1); only ancestry changed.
Scientific records, caches, source-review output, histories, regression tests, and generated pages
are unchanged. Historical validation results and recorded source/access limitations therefore
remain applicable, but required CI must pass at this new head. No new source review or local test
rerun is claimed by this ancestry-only update.

The protected main queue remains mandatory. Keep dependents on their reviewed parent until that
parent is confirmed merged; move dependents before deleting merged branches.

[realmarcin]

Self-adversarial governance integration review at exact head 8ca261ecd78cdcc2578c2eea0a269516adee2dbe. This is a COMMENT, not independent approval.

Integrated already-merged main PR #1730 (fe1752572a688051e8105e5b89d3099fe2202c63). Compared with prior reviewed head 725ec42223a8ea31e3bc7464731a1f22574d2b4c, exactly two files changed: scripts/.vendored_canon_ref and tests/test_id_label_empty_adapter.py. Each resulting tree differs from its old tree by the exact binary patch from main, and each batch-owned binary patch remains byte-identical (SHA-256 9aacaf4e78b7da4f2e1a13078691167aa72cf651f2546b1eed44f80c7821bba1). These invariants passed on all 74 published branches. Original heads are retained in local archive refs/archive/communitymech-pre-governance-20261007. No scientific record, source cache, history, decision ledger, schema, runtime code or generated page changed in this integration.

Adversarial inspection: the adapter regression still checks the empty sentinel and case-insensitive caching, now with an isolated fake oaklib module and a one-call selector assertion. No validation threshold or runtime behavior was relaxed. Fresh regressions at both stack ends: 337 passed in 214.19s (0:03:34); 917 passed in 402.58s (0:06:42). Docs-current and pinned vendored-sync passed at batches26/99. The 72 intermediate combinations were checked by tree/patch hashes, not independently retested. Historical source-review limitations and unresolved issues, including loader #1703 and cache #1091, remain applicable. This is not new paper review, independent approval, or a claim that those outstanding issues are fixed.

Digest-bound integration receipt/logs: /private/tmp/communitymech-governance-integration-20261007/receipt.json. Prior output/review records in reports/causal_graph_review/ remain unchanged. The prior lifecycle receipt is archived and will be updated only after all exact-head comments are verified.

Required CI and independent review must pass for the exact head and protected merge-queue candidate. No CI rerun, manual dispatch, fabricated status, admin merge or protection bypass. Dependents remain draft; move them before deleting a merged parent branch.

[realmarcin]

Exact-head self-adversarial restack review at e37cab3b42aaa20d7efcf4aec4b2fa08e0beed08.
COMMENT, not independent approval.

The batch-owned binary patch remains byte-identical:
SHA-256 9aacaf4e78b7da4f2e1a13078691167aa72cf651f2546b1eed44f80c7821bba1.
Tree e0991441852718c98e57b368175c2996aa3be739 matches the independently computed clean merge.
Compared with historical tree bbae8c0e9e65634607ba9ad90606d19a186d0283, only scripts/.vendored_canon_ref
changes, incorporating main PR #1834's pin 849f336e025510316a5f235eb0af8547b8bd50cc.
All curated records, source caches, review outputs, histories, regression tests, and rendered
pages remain unchanged. No new primary-source review or local scientific-test rerun is claimed.

This PR is now part of native stack #1973, rooted at #1363 on main. No protected merge
has occurred. Fresh eligible PR/merge-group CI remains mandatory. No rule bypass, fabricated
status, merge into a topic parent, or premature branch deletion.

[realmarcin]

Superseded by the protected cumulative merge #1975 at 42959bef2549f9a42c3e3303a0e10fd5be99f30e. This PR's reviewed source head 501c99ee194c48b26fb71afad541c12cd6efa04e was included in the cumulative branch; the final squash tree matches the reviewed integration tree exactly, and all seven required merge-group checks passed.

Patch-inclusion receipt. Existing issue-closing links were transferred to #1975; unresolved research and non-graph gaps are not closed by this action. This PR is being closed as superseded, not represented as individually merged. Archival provenance tags retain source commits; cleanup removes branch refs only and preserves worktree files.