{
  "generated_at": "2026-09-24T18:45:00Z",
  "source_report": "reports/paired_publications_2026-09-24.json",
  "source_review_queue": "reports/paired_publications_review_queue_2026-06-04.md",
  "decision_summary": {
    "decision": "accept",
    "groups": 88,
    "raw_candidates": 524,
    "note": "Manual review decisions accept represented GitHub release + Zenodo record relations; software-only records remain software/version metadata unless a bibliography folder is explicitly curated. R20-R24 record CEREBRUM, SIA, and On-Policy Distillation supersession/version-history decisions so newer versions do not create duplicate bibliography rows. R26-R27 record CogSecSkills and Codomyrmex version-history decisions under already-cited DOIs. R71 records the untagged Codomyrmex v1.3.0 release as already represented, and R72 records Active Fedference v1.0.4 as a version-specific artifact under its existing concept DOI without a duplicate bibliography row. R73 records the re-fingerprinted untagged Codomyrmex v1.3.0 release from the 2026-09-04 report as superseded under R71 precedent, and R74 records GNN v3.2.0 as a version-specific release of its represented work. R75-R76 record the rotating Codomyrmex draft URLs as superseded under R71/R73 precedent, and R77-R78 record the ActiveInferAnts and CEREBRUM releases as version-specific artifacts under the represented Cognitive Integrity Framework DOI after the principal classified cognitive_integrity as curated. R79 records the Cognitive Diagrams v2.5.0 release (2026-09-10 scan) as version-history-only under the already-cited concept DOI 10.5281/zenodo.19695259. R80 records the six GitHub release pairs (v0.3.0-v1) under the canonical curated EvoJump concept 10.5281/zenodo.22664675 as software-catalog (SOFTWARE.md already lists EvoJump; the citable paper remains bibliography row #12, concept 10.5281/zenodo.17229924), and R81 records the GitHub-Zenodo automated integration archive concept 10.5281/zenodo.22664645 (docxology/EvoJump-v0.5.2.zip, zip-only) as a superseded duplicate deposit. R82-R83 (2026-09-17 scan) record the fep_lean v1.2.0 and GeneralizedNotationNotation v3.4.0 releases as version-history-only under their already-cited citation DOIs (10.5281/zenodo.19699233 row #113 and 10.5281/zenodo.7803313 row #168), both pairs lacking github_release_mentions_doi cross-link evidence, so neither creates a duplicate bibliography row."
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      "decided_by": "user",
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      "title": "Transcript of Active Inference GuestStream 049.1: \"Clickbait, consciousness science, and responsible journalism\"",
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          "review_source": "user: Accept for all",
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          "review_decision": "accept",
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          "review_decision": "accept",
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      "decision": "accept",
      "decided_at": "2026-06-04T22:32:27Z",
      "decided_by": "user",
      "doi": "10.5281/zenodo.16782757",
      "title": "The Ant Stack",
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      "decided_at": "2026-06-04T22:32:27Z",
      "decided_by": "user",
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          "review_source": "user: monorepo root releases do not pair to sub-exemplar",
          "source_report": "reports/paired_publications_2026-08-19.json"
        },
        {
          "doi": "10.5281/zenodo.16903351",
          "record_title": "A template/ approach to Reproducible Generative Research: Architecture and Ergonomics from Configuration through Publication",
          "zenodo_record_url": "https://zenodo.org/records/16903351",
          "github_repo": "docxology/template",
          "github_release_url": "https://github.com/docxology/template/releases/tag/0.1",
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    {
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      "decision": "accept",
      "decided_at": "2026-08-19T22:43:14Z",
      "decided_by": "user",
      "doi": "10.5281/zenodo.21864003",
      "title": "Robust Belief Sharing in Federated Active Inference: A Recovery-Tested Generalized-Variational Framework for Categorical Contamination-Aware Consensus",
      "candidate_github_repo": "ActiveInferenceInstitute/Active_Fedference",
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      "decision": "accept",
      "decided_at": "2026-08-19T22:43:14Z",
      "decided_by": "user",
      "doi": "10.5281/zenodo.21983948",
      "title": "docxplus — the Intelligent Document Container",
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      "raw_candidates": [
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      "decided_by": "user",
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          "review_source": "user: approved all remaining review items; existing v1.3.0-paper relation remains the represented source",
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      "decided_by": "user",
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      "raw_candidates": [
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      "decided_by": "codex",
      "doi": "10.5281/zenodo.21750800",
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      "rationale": "Supersede: the docxology/codomyrmex v1.3.0 release (untagged-ce7d22a2764590b03a3d) is a software version of the already-represented Codomyrmex work; DOI 10.5281/zenodo.21750800 is indexed in data/works.json with curated folder papers/2026_Codomyrmex. Same DOI and work as R71 (untagged-c403e197e42abd3e0829 release, recorded 2026-08-26); the 2026-09-04 sync re-queued this candidate only because the release URL fingerprint differs.",
      "raw_candidate_count": 1,
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          "reason": "pair lacks DOI/release cross-link evidence required for automatic apply",
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      "decided_at": "2026-09-07T21:03:44Z",
      "decided_by": "codex",
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      "folder": "2026_GeneralizedNotationNotationGNN",
      "representation": "bibliography-folder version-history-only",
      "rationale": "Supersede: the ActiveInferenceInstitute/GeneralizedNotationNotation v3.2.0 release is a software version of the already-represented GNN work; DOI 10.5281/zenodo.7803313 is bibliography row 168 with curated folder papers/2026_GeneralizedNotationNotationGNN.",
      "raw_candidate_count": 1,
      "raw_candidates": [
        {
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          "reason": "pair lacks DOI/release cross-link evidence required for automatic apply",
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          "github_release_url": "https://github.com/ActiveInferenceInstitute/GeneralizedNotationNotation/releases/tag/v3.2.0",
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      "decided_by": "user",
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      "decided_by": "user",
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      "folder": "2026_CognitiveIntegrityFramework",
      "representation": "bibliography-folder version-history-only",
      "rationale": "Supersede: the Codomyrmex v1.2.3 draft release is version metadata under the represented Cognitive Integrity Framework Part 2 DOI 10.5281/zenodo.22134545, indexed in data/works.json with curated folder papers/2026_CognitiveIntegrityFramework. The principal confirmed the disposition in the 2026-09-07 session.",
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          "confidence": "needs_review",
          "reason": "pair lacks DOI/release cross-link evidence required for automatic apply",
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      "decided_by": "user",
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      "raw_candidate_count": 1,
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          "reason": "pair lacks DOI/release cross-link evidence required for automatic apply",
          "github_repo": "ActiveInferenceInstitute/ActiveInferAnts",
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          "zenodo_record_url": "https://zenodo.org/records/18364118",
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      "decided_by": "user",
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      "candidate_github_repo": "ActiveInferenceInstitute/CEREBRUM",
      "folder": "2026_CognitiveIntegrity",
      "representation": "bibliography-folder version-specific artifact metadata",
      "rationale": "Supersede: the CEREBRUM release 1.3 is a version-specific artifact under the represented Cognitive Integrity Framework Part 1 DOI 10.5281/zenodo.18364118 without a duplicate bibliography row (R72-style). The principal classified docxology/cognitive_integrity as curated (paper-backed) in the 2026-09-07 session.",
      "raw_candidate_count": 1,
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      "decided_by": "agent:PublicationIntake",
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      "candidate_github_repo": "docxology/cognitive_case_diagrams",
      "folder": "2026_CognitiveCaseDiagrams",
      "representation": "version-history: GitHub release v2.5.0 pairs under concept 10.5281/zenodo.19695259; bibliography row #112 already cites the concept DOI, so this release must not create a duplicate bibliography row. The concept's latest deposited version is 2.4.0 (record 22653315, 2026-09-07); when a v2.5.0 Zenodo version deposit appears it will pair under its own version DOI and can update the row normally.",
      "raw_candidates": [
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          "zenodo_record_url": "https://zenodo.org/records/19695259",
          "github_repo": "docxology/cognitive_case_diagrams",
          "github_release_url": "https://github.com/docxology/cognitive_case_diagrams/releases/tag/v2.5.0",
          "release_tag": "v2.5.0",
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          "resource_type": {
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          "review_decision": "superseded",
          "reviewed_at": "2026-09-10T17:43:49Z",
          "review_source": "agent:PublicationIntake per docs/operations/publication-sync.md manual review path: work already represented by row #112 citing the exact concept DOI in the pair; release v2.5.0 (2026-09-08) is from the same repo the concept record links isSupplementTo; no duplicate row",
          "source_report": "reports/paired_publications_2026-09-10.json"
        }
      ],
      "raw_candidate_count": 1
    },
    {
      "id": "R80",
      "decision": "accept",
      "decided_at": "2026-09-11T16:37:44Z",
      "decided_by": "agent:orchestrator",
      "doi": "10.5281/zenodo.22664675",
      "title": "EvoJump: A Comprehensive Framework for Evolutionary Ontogenetic Analysis",
      "candidate_github_repo": "docxology/EvoJump",
      "folder": "",
      "representation": "software-catalog: 6 GitHub release pairs (v0.3.0-v1) under concept 10.5281/zenodo.22664675; the EvoJump software work is already represented in pages/SOFTWARE.md and the citable paper is bibliography row #12 (concept 10.5281/zenodo.17229924, papers/2025_EvoJump), so these software release deposits must not create a duplicate bibliography row",
      "rationale": "Accept as software-catalog: concept 10.5281/zenodo.22664675 (latest version record 22667290, v0.5.2) is the canonical curated deposit — the repo README citation section links this concept DOI (release v0.5.1 body) and it is the only pairing with DOI/release cross-link evidence (github_release_mentions_doi). The deposit archives the source snapshot plus the compiled evojump_paper.pdf; the paper remains represented by bibliography row #12 (2025 concept 10.5281/zenodo.17229924). Software-only deposit: SOFTWARE.md representation, no new bibliography folder (R02 precedent).",
      "raw_candidate_count": 6,
      "raw_candidates": [
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          "reason": "pair lacks DOI/release cross-link evidence required for automatic apply",
          "github_repo": "docxology/EvoJump",
          "github_release_url": "https://github.com/docxology/EvoJump/releases/tag/v0.3.0",
          "zenodo_record_url": "https://zenodo.org/records/22664675",
          "release_tag": "v0.3.0",
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          "review_decision": "accept",
          "reviewed_at": "2026-09-11T16:37:44Z",
          "review_source": "user: 2026-09-11 EvoJump needs_review cluster review (principal-directed batch); canonical curated concept deposit (README-cited; source archive + evojump_paper.pdf) represented in pages/SOFTWARE.md; paper citation remains bibliography row #12 (concept 10.5281/zenodo.17229924)",
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        {
          "action_type": "needs_review",
          "doi": "10.5281/zenodo.22664675",
          "title": "EvoJump: A Comprehensive Framework for Evolutionary Ontogenetic Analysis",
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          "reason": "pair lacks DOI/release cross-link evidence required for automatic apply",
          "github_repo": "docxology/EvoJump",
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          "zenodo_record_url": "https://zenodo.org/records/22664675",
          "release_tag": "v0.4.0",
          "folder": "2026_EvoJump",
          "review_decision": "accept",
          "reviewed_at": "2026-09-11T16:37:44Z",
          "review_source": "user: 2026-09-11 EvoJump needs_review cluster review (principal-directed batch); canonical curated concept deposit (README-cited; source archive + evojump_paper.pdf) represented in pages/SOFTWARE.md; paper citation remains bibliography row #12 (concept 10.5281/zenodo.17229924)",
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        {
          "action_type": "needs_review",
          "doi": "10.5281/zenodo.22664675",
          "title": "EvoJump: A Comprehensive Framework for Evolutionary Ontogenetic Analysis",
          "confidence": "needs_review",
          "reason": "pair lacks DOI/release cross-link evidence required for automatic apply",
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          "zenodo_record_url": "https://zenodo.org/records/22664675",
          "release_tag": "v0.5.0",
          "folder": "2026_EvoJump",
          "review_decision": "accept",
          "reviewed_at": "2026-09-11T16:37:44Z",
          "review_source": "user: 2026-09-11 EvoJump needs_review cluster review (principal-directed batch); canonical curated concept deposit (README-cited; source archive + evojump_paper.pdf) represented in pages/SOFTWARE.md; paper citation remains bibliography row #12 (concept 10.5281/zenodo.17229924)",
          "source_report": "reports/paired_publications_2026-09-10.json"
        },
        {
          "action_type": "needs_review",
          "doi": "10.5281/zenodo.22664675",
          "title": "EvoJump: A Comprehensive Framework for Evolutionary Ontogenetic Analysis",
          "confidence": "strong",
          "reason": "new pair is strong, but type or domain cannot be inferred safely",
          "github_repo": "docxology/EvoJump",
          "github_release_url": "https://github.com/docxology/EvoJump/releases/tag/v0.5.1",
          "zenodo_record_url": "https://zenodo.org/records/22664675",
          "release_tag": "v0.5.1",
          "folder": "2026_EvoJump",
          "review_decision": "accept",
          "reviewed_at": "2026-09-11T16:37:44Z",
          "review_source": "user: 2026-09-11 EvoJump needs_review cluster review (principal-directed batch); canonical curated concept deposit (README-cited; source archive + evojump_paper.pdf) represented in pages/SOFTWARE.md; paper citation remains bibliography row #12 (concept 10.5281/zenodo.17229924)",
          "source_report": "reports/paired_publications_2026-09-10.json"
        },
        {
          "action_type": "needs_review",
          "doi": "10.5281/zenodo.22664675",
          "title": "EvoJump: A Comprehensive Framework for Evolutionary Ontogenetic Analysis",
          "confidence": "needs_review",
          "reason": "pair lacks DOI/release cross-link evidence required for automatic apply",
          "github_repo": "docxology/EvoJump",
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          "zenodo_record_url": "https://zenodo.org/records/22664675",
          "release_tag": "v0.5.2",
          "folder": "2026_EvoJump",
          "review_decision": "accept",
          "reviewed_at": "2026-09-11T16:37:44Z",
          "review_source": "user: 2026-09-11 EvoJump needs_review cluster review (principal-directed batch); canonical curated concept deposit (README-cited; source archive + evojump_paper.pdf) represented in pages/SOFTWARE.md; paper citation remains bibliography row #12 (concept 10.5281/zenodo.17229924)",
          "source_report": "reports/paired_publications_2026-09-10.json"
        },
        {
          "action_type": "needs_review",
          "doi": "10.5281/zenodo.22664675",
          "title": "EvoJump: A Comprehensive Framework for Evolutionary Ontogenetic Analysis",
          "confidence": "needs_review",
          "reason": "pair lacks DOI/release cross-link evidence required for automatic apply",
          "github_repo": "docxology/EvoJump",
          "github_release_url": "https://github.com/docxology/EvoJump/releases/tag/v1",
          "zenodo_record_url": "https://zenodo.org/records/22664675",
          "release_tag": "v1",
          "folder": "2026_EvoJump",
          "review_decision": "accept",
          "reviewed_at": "2026-09-11T16:37:44Z",
          "review_source": "user: 2026-09-11 EvoJump needs_review cluster review (principal-directed batch); canonical curated concept deposit (README-cited; source archive + evojump_paper.pdf) represented in pages/SOFTWARE.md; paper citation remains bibliography row #12 (concept 10.5281/zenodo.17229924)",
          "source_report": "reports/paired_publications_2026-09-10.json"
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    },
    {
      "id": "R81",
      "decision": "superseded",
      "decided_at": "2026-09-11T16:37:44Z",
      "decided_by": "agent:orchestrator",
      "doi": "10.5281/zenodo.22664645",
      "title": "EvoJump: A Comprehensive Framework for Evolutionary Ontogenetic Analysis",
      "candidate_github_repo": "docxology/EvoJump",
      "folder": "",
      "representation": "superseded duplicate deposit: GitHub-Zenodo automated integration archive of docxology/EvoJump (single file docxology/EvoJump-v0.5.2.zip, the {owner}/{repo}-{tag}.zip integration naming); the canonical curated deposit is concept 10.5281/zenodo.22664675 (source archive + evojump_paper.pdf, linked by the repo README citation), so these auto-archive pairs must not create any row",
      "rationale": "Supersede: concept 10.5281/zenodo.22664645 (latest version record 22667291, v0.5.2) is the GitHub-Zenodo automated integration archive of docxology/EvoJump — its only file is docxology/EvoJump-v0.5.2.zip, matching the integration naming pattern of GNN, CogSecSkills, and docxology/template archives. It contains no paper PDF. The canonical curated deposit is concept 10.5281/zenodo.22664675, named by the README citation and the only github_release_mentions_doi cross-link in the 462-pair scan.",
      "raw_candidate_count": 6,
      "raw_candidates": [
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          "title": "EvoJump: A Comprehensive Framework for Evolutionary Ontogenetic Analysis",
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          "reason": "pair lacks DOI/release cross-link evidence required for automatic apply",
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          "review_source": "user: 2026-09-11 EvoJump needs_review cluster review (principal-directed batch); GitHub-Zenodo automated integration archive (docxology/EvoJump-v0.5.2.zip) superseded by the canonical curated concept 10.5281/zenodo.22664675",
          "source_report": "reports/paired_publications_2026-09-10.json"
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    {
      "id": "R82",
      "decision": "accept",
      "decided_at": "2026-09-17T23:18:16Z",
      "decided_by": "agent:orchestrator",
      "doi": "10.5281/zenodo.19699233",
      "title": "Towards Lean 4 Formalization of the Free Energy Principle: AI-Driven Theorem Sketching and Verification for Active Inference and Bayesian Mechanics",
      "candidate_github_repo": "ActiveInferenceInstitute/fep_lean",
      "folder": "2026_FEPLean",
      "representation": "version-history-only: GitHub release ActiveInferenceInstitute/fep_lean v1.2.0 pairs to the already-cited FEP-lean formalization record without github_release_mentions_doi cross-link evidence, so no automatic update applies; the work is already represented as bibliography row #113 (papers/2026_FEPLean, citation DOI 10.5281/zenodo.19699233) with the v1.1.0 artifact DOI 10.5281/zenodo.22072956 recorded in the pages/SOFTWARE.md AII row, and the v1.2.0 release is version history under the existing citation DOI — no duplicate bibliography row",
      "rationale": "Accept as version-history-only: bibliography row #113 cites concept DOI 10.5281/zenodo.19699233 with folder 2026_FEPLean, and the 2026-09-17 scan pairs the newer fep_lean v1.2.0 release to that same record while the release-vs-record cross-link (github_release_mentions_doi) is absent, so the tool correctly defers it. No newer version DOI evidence is present in the scan, so no row, folder, or artifact-DOI change is warranted; recording the pair keeps future scans reporting already_reviewed.",
      "raw_candidate_count": 1,
      "raw_candidates": [
        {
          "action_type": "needs_review",
          "doi": "10.5281/zenodo.19699233",
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          "confidence": "needs_review",
          "reason": "pair lacks DOI/release cross-link evidence required for automatic apply",
          "github_repo": "ActiveInferenceInstitute/fep_lean",
          "github_release_url": "https://github.com/ActiveInferenceInstitute/fep_lean/releases/tag/v1.2.0",
          "zenodo_record_url": "https://zenodo.org/records/19699233",
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          "folder": "2026_FEPLean",
          "review_decision": "accept",
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          "review_source": "agent:orchestrator: manual review of reports/paired_publications_2026-09-17.json — work already represented under the paired citation DOI (bibliography rows #113 / #168); release lacks cross-link evidence, recorded as version-history-only",
          "source_report": "reports/paired_publications_2026-09-17.json"
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    {
      "id": "R83",
      "decision": "accept",
      "decided_at": "2026-09-17T23:18:16Z",
      "decided_by": "agent:orchestrator",
      "doi": "10.5281/zenodo.7803313",
      "title": "GeneralizedNotationNotation (GNN)",
      "candidate_github_repo": "ActiveInferenceInstitute/GeneralizedNotationNotation",
      "folder": "2026_GeneralizedNotationNotationGNN",
      "representation": "version-history-only: GitHub release ActiveInferenceInstitute/GeneralizedNotationNotation v3.4.0 pairs to the already-cited GNN record without github_release_mentions_doi cross-link evidence, so no automatic update applies; the work is already represented as bibliography row #168 (papers/2026_GeneralizedNotationNotationGNN, DOI 10.5281/zenodo.7803313) and the separate software DOI 10.5281/zenodo.19600217 is already recorded in the pages/SOFTWARE.md AII row — the v3.4.0 release is version history under the existing citation DOI, no duplicate bibliography row",
      "rationale": "Accept as version-history-only: bibliography row #168 cites 10.5281/zenodo.7803313 with folder 2026_GeneralizedNotationNotationGNN, and the 2026-09-17 scan pairs the newer GNN v3.4.0 release to that same record while the release-vs-record cross-link (github_release_mentions_doi) is absent, so the tool correctly defers it. No newer version DOI evidence is present in the scan, so no row, folder, or software-DOI change is warranted; recording the pair keeps future scans reporting already_reviewed.",
      "raw_candidate_count": 1,
      "raw_candidates": [
        {
          "action_type": "needs_review",
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          "confidence": "needs_review",
          "reason": "pair lacks DOI/release cross-link evidence required for automatic apply",
          "github_repo": "ActiveInferenceInstitute/GeneralizedNotationNotation",
          "github_release_url": "https://github.com/ActiveInferenceInstitute/GeneralizedNotationNotation/releases/tag/v3.4.0",
          "zenodo_record_url": "https://zenodo.org/records/7803313",
          "release_tag": "v3.4.0",
          "folder": "2026_GeneralizedNotationNotationGNN",
          "review_decision": "accept",
          "reviewed_at": "2026-09-17T23:18:16Z",
          "review_source": "agent:orchestrator: manual review of reports/paired_publications_2026-09-17.json — work already represented under the paired citation DOI (bibliography rows #113 / #168); release lacks cross-link evidence, recorded as version-history-only",
          "source_report": "reports/paired_publications_2026-09-17.json"
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    {
      "id": "R84",
      "decision": "accept",
      "decided_at": "2026-09-24T18:45:00Z",
      "decided_by": "agent:orchestrator",
      "doi": "10.5281/zenodo.8228934",
      "title": "Transcript of Active Inference GuestStream 049.1: \"Clickbait, consciousness science, and responsible journalism\"",
      "candidate_github_repo": "ActiveInferenceInstitute/Active_InferAnts",
      "folder": "2023_TranscriptActiveInference",
      "representation": "bibliography-folder",
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      "raw_candidate_count": 1,
      "raw_candidates": [
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          "zenodo_record_url": "https://zenodo.org/records/8228934",
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          "release_tag": "1",
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          "raw_confidence": "needs_review",
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          "review_decision": "accept",
          "reviewed_at": "2026-09-24T18:45:00Z",
          "review_source": "orchestrator: work already represented in the curated bibliography at the cited DOI (see note); dispositions per docs/operations/publication-sync.md Manual Review Path",
          "source_report": "reports/paired_publications_2026-09-24.json"
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    {
      "id": "R85",
      "decision": "accept",
      "decided_at": "2026-09-24T18:45:00Z",
      "decided_by": "agent:orchestrator",
      "doi": "10.5281/zenodo.19699233",
      "title": "Towards Lean 4 Formalization of the Free Energy Principle: AI-Driven Theorem Sketching and Verification for Active Inference and Bayesian Mechanics",
      "candidate_github_repo": "ActiveInferenceInstitute/fep_formal",
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    {
      "id": "R86",
      "decision": "accept",
      "decided_at": "2026-09-24T18:45:00Z",
      "decided_by": "agent:orchestrator",
      "doi": "10.5281/zenodo.18364118",
      "title": "Cognitive Integrity Framework: Formal Foundations (Part 1 of 3: Theoretical Foundations)",
      "candidate_github_repo": "ActiveInferenceInstitute/Active_InferAnts",
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