feat(phd-phase1-unify-1-6): \citetheorem{INV-k} macro + canonical labels in appendix F#603
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…els in appendix F [agent=phase1-unify-1-6]
Phase 1 UNIFY · trios#380 task 1.6 — \citetheorem{INV-k} resolution through AP.F.
Problem: chapters cite Coq invariants "INV-k" as bare text or with the
ad-hoc stub \citetheorem already present only in defense/slides.tex
(\newcommand{\citetheorem}[1]{[\textsc{#1}]}). No corpus-wide robust
hyperref existed and appendix F-coq-citation-map.tex carried no
\label{thm:INV-k} anchors, so cross-references between body and the
canonical Coq citation map were dead text.
Fix: define \citetheorem{INV-k} as a single \providecommand in main.tex
and main_ru.tex that hyperrefs into appendix F via \label{thm:INV-k}.
Add \label{thm:INV-N} to every row of the INV summary table in F (8 rows
present + 5 added for INV-{6,9,13,22,23} that are mentioned in chapters).
Notes:
- \providecommand (not \newcommand) is intentional: the existing slide
stub in defense/slides.tex remains the active definition when slides.tex
compiles standalone, while main.tex now provides the canonical hyperref
resolution for the full monograph build.
- INV-{9,13,22,23} are not yet primary records in assertions/igla_assertions.json
so their F rows read 'registry-only' / 'no .v anchor' — honest per R5.
- All 13 distinct INV-N referenced in chapters now resolve to a label.
Inventory check (post-patch):
Total \label sites: 1158 (was 1145; +13 new thm:INV-* labels)
Unique label keys: 1158 (still 0 duplicates)
Dangling \ref: 0
Original 119 referenced keys: 119/119 still resolve
New file: docs/phd/citetheorem-map.md — INV->file audit map (83 lines).
Stacked on feat/phd-phase1-unify-1-5 (PR #602, task 1.5).
Skill: phd-chapter-author v1.1 + phd-monograph-auditor v1.2.
Anchor: phi^2 + phi^-2 = 3, DOI 10.5281/zenodo.19227877.
R1 (no .py/.sh): patch script ran from /tmp/, only LaTeX + Markdown committed.
R5 (honesty): registry-only INVs explicitly flagged, no fabrication.
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…or headers in 70 chapters [agent=phase1-unify-1-4] Phase 1 UNIFY · trios#380 task 1.4 — header blocks (~0.5 pp/ch). Per #380 manifest (PART VIII Flos Aureus, 34 chapters), every chapter must carry a branded header naming its golden-flower petal: FA.00 Monad / FA.01 Golden Egg / FA.02 Golden Cut / ... / FA.33 Epilogue, grouped into the 8 Parts of the Flos Aureus strand: Part I Foundations (fa_00..fa_03) Part II Expansion (fa_04..fa_07) Part III Crystal (fa_08..fa_09) Part IV Synthesis (fa_10) Part V Sacred Geometry (fa_11..fa_19) Part VI Physics Foundation (fa_20..fa_24) Part VII Algebraic Proofs (fa_25..fa_29) Part VIII Imagery & Genealogy (fa_30..fa_33) Two distinct header palettes: - Flos Aureus (yellow!4 / yellow!50!brown) for fa_NN: title carries petal name (e.g. 'Flos Aureus FA.05 Golden Bridge'), motif, Part, Lane, theorem count, Coq link, notation key. - Trinity S^3AI Strand (blue!3 / blue!40!black) for ch_NN: title carries chapter number, anchor, lane S<n>, theorem count, Coq link. Fields present in both palettes: anchor phi^2+phi^-2=3 (Trinity Identity, INV-22) + INV-k cross-reference via \citetheorem (task 1.6). Coverage: Patched: 68 chapters (34 fa_NN + 34 ch_NN with NN in 01..34) Skipped (bespoke pre-existing): ch_00, ch_35_mesh_node — left intact per R6 lane discipline. Total with Chapter Anchor: 70/70 = 100% coverage. Cross-check vs task 1.5/1.6 invariants (post amend): - Total \label sites: 1158 (unchanged) - Duplicate keys: 0 - Dangling refs: 0 - 119/119 referenced keys preserved New file: docs/phd/chapter-headers-audit.md (142 lines) — Flos Aureus manifest table + Trinity strand table + per-chapter audit with file/lane/petal/motif/theorem-count/header-presence. Stacked on feat/phd-phase1-unify-1-6 (PR #603). Skill: phd-chapter-author v1.1 + phd-monograph-auditor v1.2. Anchor: phi^2 + phi^-2 = 3, DOI 10.5281/zenodo.19227877. R1 (no .py/.sh committed). R5 (honesty): theorem counts mechanical; stub chapters honestly report 0; chapters without dedicated .v use per-theorem fallback link. R6 (lane discipline): no chapter prose touched; only header injection. R10 (atomic): one amended commit.
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…or headers in 70 chapters (#725) * feat(phd-phase1-unify-1-2): rename Flos Aureus strand NN-slug.tex -> fa_NN.tex (34 files) [agent=perplexity-computer-phase1] Phase 1 UNIFY · trios#380 task 1.2. Pure git-mv rename: each docs/phd/chapters/NN-<slug>.tex moves to docs/phd/chapters/fa_NN.tex with 100% file similarity (R == 100). No content edits in this commit; the rename is paired 1:1 with main.tex include-path patches in the next commit. Why: per #380 manifest task 1.2, the named-strand canonical namespace is fa_NN (Flos Aureus), parallel to the ch_NN namespace (Trinity S³AI). phd-chapter-author v1.1 lessons-learned point 1 already classified the old NN-slug names as the canonical chapter location, but the v6.2 manifest reserves the unprefixed NN-slug namespace and instead pins fa_NN as the namespace shared by main.tex include lines and Neon ssot.chapters export targets. Mechanical mapping (NN preserved, slug dropped): 00-monad.tex -> fa_00.tex 01-golden-egg.tex -> fa_01.tex ... 33-epilogue.tex -> fa_33.tex Anchor phi^2 + phi^{-2} = 3 · DOI 10.5281/zenodo.19227877. Refs trios#380 Phase 1 UNIFY task 1.2. * feat(phd-phase1-unify-1-2): main.tex + main_ru.tex include paths -> fa_NN [agent=perplexity-computer-phase1] Phase 1 UNIFY · trios#380 task 1.2 (paired with previous 34-file git-mv commit). Patches: - docs/phd/main.tex line 299..353: 34 \include{chapters/NN-slug} -> \include{chapters/fa_NN}. The Trinity S³AI strand (\include{chapters/ch_00..ch_34}, lines 357..391) is unchanged. - docs/phd/main_ru.tex: same 34 substitutions. Verification: - grep -cE "chapters/fa_" main.tex == 34 (target) - grep -cE "chapters/ch_" main.tex == 35 (preserved Trinity S³AI) - grep -cE "chapters/[0-9]{2}-" main.tex == 0 (no stale refs) - repo-wide grep across .rs/.toml/.ts/.py/.yml/.yaml/.json for "chapters/NN-slug.tex" returns 0 hits. - tools/citetheorem_audit/src/lib.rs uses bare "NN-slug.tex" strings inside #[cfg(test)] tempdir-scoped tests; those names are test-data only and do not reach the real chapters directory, so they remain untouched (out of scope for task 1.2 — the test data set will be revisited in task 1.5 cross-reference sweep). Anchor phi^2 + phi^{-2} = 3 · DOI 10.5281/zenodo.19227877. Refs trios#380 Phase 1 UNIFY task 1.2. * feat(phd-phase1-unify-1-5): chapter-prefix non-referenced \label keys; eliminate LaTeX duplicate-label warnings [agent=phase1-unify-1-5] Phase 1 UNIFY · trios#380 task 1.5 — cross-references sweep. Problem: 70 chapter files in docs/phd/chapters/ (34 ch_NN + 35 fa_NN + ch_35_mesh_node) defined ~126 label keys identically across multiple files (e.g. \label{abstract}, \label{introduction}, \label{sec:05-intro}). None of these duplicate keys were consumed by any \ref/\autoref/\eqref/ \Cref/\pageref in the corpus, so they were pure LaTeX duplicate-label warnings — not broken cross-references. Still, they bloated the build log and made the PDF build noisy on the road to defense 2026-06-15. Fix: for every \label{KEY} in <stem>.tex, if KEY is consumed by any \ref-family command anywhere in docs/phd/, leave it bare (protected); otherwise rewrite to \label{<stem>:KEY}. Idempotent: skip keys already prefixed. Mechanical rename, no semantic content changed. Inventory before patch: - 1145 total \label sites, 620 unique keys - 126 duplicate keys (all unreferenced) - 119 referenced keys (all uniquely defined, 0 dangling) Inventory after patch: - 1145 total \label sites, 1145 unique keys - 0 duplicate keys - 0 dangling refs - 119/119 originally-referenced keys still resolve (no breakage) Patched 1011 \label sites across 70 files. Added docs/phd/cross-ref-audit.md with full label→file map (1324 lines) satisfying acceptance criterion #1 of #380 task 1.5. Stacked on feat/phd-phase1-unify-1-2 (PR #595, task 1.2). Skill: phd-chapter-author v1.1 + phd-monograph-auditor v1.2. Anchor: phi^2 + phi^-2 = 3, DOI 10.5281/zenodo.19227877. R1 (no .py/.sh committed): the patch script ran from /tmp, only LaTeX changed. * feat(phd-phase1-unify-1-6): \citetheorem{INV-k} macro + canonical labels in appendix F [agent=phase1-unify-1-6] Phase 1 UNIFY · trios#380 task 1.6 — \citetheorem{INV-k} resolution through AP.F. Problem: chapters cite Coq invariants "INV-k" as bare text or with the ad-hoc stub \citetheorem already present only in defense/slides.tex (\newcommand{\citetheorem}[1]{[\textsc{#1}]}). No corpus-wide robust hyperref existed and appendix F-coq-citation-map.tex carried no \label{thm:INV-k} anchors, so cross-references between body and the canonical Coq citation map were dead text. Fix: define \citetheorem{INV-k} as a single \providecommand in main.tex and main_ru.tex that hyperrefs into appendix F via \label{thm:INV-k}. Add \label{thm:INV-N} to every row of the INV summary table in F (8 rows present + 5 added for INV-{6,9,13,22,23} that are mentioned in chapters). Notes: - \providecommand (not \newcommand) is intentional: the existing slide stub in defense/slides.tex remains the active definition when slides.tex compiles standalone, while main.tex now provides the canonical hyperref resolution for the full monograph build. - INV-{9,13,22,23} are not yet primary records in assertions/igla_assertions.json so their F rows read 'registry-only' / 'no .v anchor' — honest per R5. - All 13 distinct INV-N referenced in chapters now resolve to a label. Inventory check (post-patch): Total \label sites: 1158 (was 1145; +13 new thm:INV-* labels) Unique label keys: 1158 (still 0 duplicates) Dangling \ref: 0 Original 119 referenced keys: 119/119 still resolve New file: docs/phd/citetheorem-map.md — INV->file audit map (83 lines). Stacked on feat/phd-phase1-unify-1-5 (PR #602, task 1.5). Skill: phd-chapter-author v1.1 + phd-monograph-auditor v1.2. Anchor: phi^2 + phi^-2 = 3, DOI 10.5281/zenodo.19227877. R1 (no .py/.sh): patch script ran from /tmp/, only LaTeX + Markdown committed. R5 (honesty): registry-only INVs explicitly flagged, no fabrication. * feat(phd-phase1-unify-1-4): Flos Aureus & Trinity-strand Chapter Anchor headers in 70 chapters [agent=phase1-unify-1-4] Phase 1 UNIFY · trios#380 task 1.4 — header blocks (~0.5 pp/ch). Per #380 manifest (PART VIII Flos Aureus, 34 chapters), every chapter must carry a branded header naming its golden-flower petal: FA.00 Monad / FA.01 Golden Egg / FA.02 Golden Cut / ... / FA.33 Epilogue, grouped into the 8 Parts of the Flos Aureus strand: Part I Foundations (fa_00..fa_03) Part II Expansion (fa_04..fa_07) Part III Crystal (fa_08..fa_09) Part IV Synthesis (fa_10) Part V Sacred Geometry (fa_11..fa_19) Part VI Physics Foundation (fa_20..fa_24) Part VII Algebraic Proofs (fa_25..fa_29) Part VIII Imagery & Genealogy (fa_30..fa_33) Two distinct header palettes: - Flos Aureus (yellow!4 / yellow!50!brown) for fa_NN: title carries petal name (e.g. 'Flos Aureus FA.05 Golden Bridge'), motif, Part, Lane, theorem count, Coq link, notation key. - Trinity S^3AI Strand (blue!3 / blue!40!black) for ch_NN: title carries chapter number, anchor, lane S<n>, theorem count, Coq link. Fields present in both palettes: anchor phi^2+phi^-2=3 (Trinity Identity, INV-22) + INV-k cross-reference via \citetheorem (task 1.6). Coverage: Patched: 68 chapters (34 fa_NN + 34 ch_NN with NN in 01..34) Skipped (bespoke pre-existing): ch_00, ch_35_mesh_node — left intact per R6 lane discipline. Total with Chapter Anchor: 70/70 = 100% coverage. Cross-check vs task 1.5/1.6 invariants (post amend): - Total \label sites: 1158 (unchanged) - Duplicate keys: 0 - Dangling refs: 0 - 119/119 referenced keys preserved New file: docs/phd/chapter-headers-audit.md (142 lines) — Flos Aureus manifest table + Trinity strand table + per-chapter audit with file/lane/petal/motif/theorem-count/header-presence. Stacked on feat/phd-phase1-unify-1-6 (PR #603). Skill: phd-chapter-author v1.1 + phd-monograph-auditor v1.2. Anchor: phi^2 + phi^-2 = 3, DOI 10.5281/zenodo.19227877. R1 (no .py/.sh committed). R5 (honesty): theorem counts mechanical; stub chapters honestly report 0; chapters without dedicated .v use per-theorem fallback link. R6 (lane discipline): no chapter prose touched; only header injection. R10 (atomic): one amended commit. * feat(phd-phase2-stubkill-2-6): expand AP.G Data Availability — INV-1..15 catalogue, falsification witnesses, INV-7 pre-reg, AVL/INV bridge [agent=phase2-2-6] (#608) - Pre-patch: 6,662 B / 152 lines, §G.1..G.6, mixed INV/AVL semantics - Post-patch: 18,560 B / 342 lines, §G.1..G.10 + §G.6.bis (+178%) R5-honest namespace separation: - AP.G's local 'INV-1..INV-7' renamed to AVL-1..AVL-7 (Available-data reproducibility invariants — SHA / grep / DOI resolution) - Appendix F's 13 Coq invariants kept under INV-N namespace (formal Coq theorems with Proven/Admitted/wip status from assertions/igla_assertions.json) - Clarifying note inserted in §G.3; §G.10 is the explicit bridge New sections: - §G.6.bis Per-invariant SHA-256 ledger (ACM AE Reusable schema) - §G.7 Coq Invariant Catalogue (13 rows verbatim from JSON registry) - §G.7 Honest-Admitted budget breakdown (3 files, 5 theorems = max 5) - §G.8 Falsification witnesses (7 INV-1..INV-7 entries verbatim from _metadata.falsification_witnesses) - §G.9 INV-7 pre-registration block (anti-HARKing seal: H_7 hypothesis, alpha=0.01, mu_0=1.55, 7 refuting conditions from JSON pre-registration) - §G.10 Appendix F <-> JSON-registry cross-reference (16 rows: 13 F-listed + 3 JSON-only wip rows: INV-6-HybridQkGain, INV-14, INV-15) Cross-reference audit (re-run): 1158 \label sites, 0 duplicates, 0 dangling refs, 119/119 referenced keys preserved (Phase 1 baseline held; new \ref{app:F}, \ref{app:falsification}, \ref{app:acm-ae} all resolve). Phase 2 STUB-KILL exit criterion satisfied for AP.G: \u22658KB target met (now 18,560 B, +178% over pre-patch). Anchor: phi^2 + phi^-2 = 3 - Zenodo DOI 10.5281/zenodo.19227877 - defense 2026-06-15. Author: Dmitrii Vasilev <raoffonom@icloud.com> (ORCID 0009-0008-4294-6159) Skill: phd-monograph-auditor v1.2 + phd-chapter-author v1.1 + autonomous-research-loop Issue: #380 (Phase 2 task 2.6) Claim: #380 (comment)
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…or headers in 70 chapters [agent=phase1-unify-1-4] Phase 1 UNIFY · trios#380 task 1.4 — header blocks (~0.5 pp/ch). Per #380 manifest (PART VIII Flos Aureus, 34 chapters), every chapter must carry a branded header naming its golden-flower petal: FA.00 Monad / FA.01 Golden Egg / FA.02 Golden Cut / ... / FA.33 Epilogue, grouped into the 8 Parts of the Flos Aureus strand: Part I Foundations (fa_00..fa_03) Part II Expansion (fa_04..fa_07) Part III Crystal (fa_08..fa_09) Part IV Synthesis (fa_10) Part V Sacred Geometry (fa_11..fa_19) Part VI Physics Foundation (fa_20..fa_24) Part VII Algebraic Proofs (fa_25..fa_29) Part VIII Imagery & Genealogy (fa_30..fa_33) Two distinct header palettes: - Flos Aureus (yellow!4 / yellow!50!brown) for fa_NN: title carries petal name (e.g. 'Flos Aureus FA.05 Golden Bridge'), motif, Part, Lane, theorem count, Coq link, notation key. - Trinity S^3AI Strand (blue!3 / blue!40!black) for ch_NN: title carries chapter number, anchor, lane S<n>, theorem count, Coq link. Fields present in both palettes: anchor phi^2+phi^-2=3 (Trinity Identity, INV-22) + INV-k cross-reference via \citetheorem (task 1.6). Coverage: Patched: 68 chapters (34 fa_NN + 34 ch_NN with NN in 01..34) Skipped (bespoke pre-existing): ch_00, ch_35_mesh_node — left intact per R6 lane discipline. Total with Chapter Anchor: 70/70 = 100% coverage. Cross-check vs task 1.5/1.6 invariants (post amend): - Total \label sites: 1158 (unchanged) - Duplicate keys: 0 - Dangling refs: 0 - 119/119 referenced keys preserved New file: docs/phd/chapter-headers-audit.md (142 lines) — Flos Aureus manifest table + Trinity strand table + per-chapter audit with file/lane/petal/motif/theorem-count/header-presence. Stacked on feat/phd-phase1-unify-1-6 (PR #603). Skill: phd-chapter-author v1.1 + phd-monograph-auditor v1.2. Anchor: phi^2 + phi^-2 = 3, DOI 10.5281/zenodo.19227877. R1 (no .py/.sh committed). R5 (honesty): theorem counts mechanical; stub chapters honestly report 0; chapters without dedicated .v use per-theorem fallback link. R6 (lane discipline): no chapter prose touched; only header injection. R10 (atomic): one amended commit.
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…t verifier (R1 fix), licence matrix, chapter↔DOI bridge, SHA cross-link, longevity policy (#726) * feat(phd-phase1-unify-1-2): rename Flos Aureus strand NN-slug.tex -> fa_NN.tex (34 files) [agent=perplexity-computer-phase1] Phase 1 UNIFY · trios#380 task 1.2. Pure git-mv rename: each docs/phd/chapters/NN-<slug>.tex moves to docs/phd/chapters/fa_NN.tex with 100% file similarity (R == 100). No content edits in this commit; the rename is paired 1:1 with main.tex include-path patches in the next commit. Why: per #380 manifest task 1.2, the named-strand canonical namespace is fa_NN (Flos Aureus), parallel to the ch_NN namespace (Trinity S³AI). phd-chapter-author v1.1 lessons-learned point 1 already classified the old NN-slug names as the canonical chapter location, but the v6.2 manifest reserves the unprefixed NN-slug namespace and instead pins fa_NN as the namespace shared by main.tex include lines and Neon ssot.chapters export targets. Mechanical mapping (NN preserved, slug dropped): 00-monad.tex -> fa_00.tex 01-golden-egg.tex -> fa_01.tex ... 33-epilogue.tex -> fa_33.tex Anchor phi^2 + phi^{-2} = 3 · DOI 10.5281/zenodo.19227877. Refs trios#380 Phase 1 UNIFY task 1.2. * feat(phd-phase1-unify-1-5): chapter-prefix non-referenced \label keys; eliminate LaTeX duplicate-label warnings [agent=phase1-unify-1-5] Phase 1 UNIFY · trios#380 task 1.5 — cross-references sweep. Problem: 70 chapter files in docs/phd/chapters/ (34 ch_NN + 35 fa_NN + ch_35_mesh_node) defined ~126 label keys identically across multiple files (e.g. \label{abstract}, \label{introduction}, \label{sec:05-intro}). None of these duplicate keys were consumed by any \ref/\autoref/\eqref/ \Cref/\pageref in the corpus, so they were pure LaTeX duplicate-label warnings — not broken cross-references. Still, they bloated the build log and made the PDF build noisy on the road to defense 2026-06-15. Fix: for every \label{KEY} in <stem>.tex, if KEY is consumed by any \ref-family command anywhere in docs/phd/, leave it bare (protected); otherwise rewrite to \label{<stem>:KEY}. Idempotent: skip keys already prefixed. Mechanical rename, no semantic content changed. Inventory before patch: - 1145 total \label sites, 620 unique keys - 126 duplicate keys (all unreferenced) - 119 referenced keys (all uniquely defined, 0 dangling) Inventory after patch: - 1145 total \label sites, 1145 unique keys - 0 duplicate keys - 0 dangling refs - 119/119 originally-referenced keys still resolve (no breakage) Patched 1011 \label sites across 70 files. Added docs/phd/cross-ref-audit.md with full label→file map (1324 lines) satisfying acceptance criterion #1 of #380 task 1.5. Stacked on feat/phd-phase1-unify-1-2 (PR #595, task 1.2). Skill: phd-chapter-author v1.1 + phd-monograph-auditor v1.2. Anchor: phi^2 + phi^-2 = 3, DOI 10.5281/zenodo.19227877. R1 (no .py/.sh committed): the patch script ran from /tmp, only LaTeX changed. * feat(phd-phase1-unify-1-4): Flos Aureus & Trinity-strand Chapter Anchor headers in 70 chapters [agent=phase1-unify-1-4] Phase 1 UNIFY · trios#380 task 1.4 — header blocks (~0.5 pp/ch). Per #380 manifest (PART VIII Flos Aureus, 34 chapters), every chapter must carry a branded header naming its golden-flower petal: FA.00 Monad / FA.01 Golden Egg / FA.02 Golden Cut / ... / FA.33 Epilogue, grouped into the 8 Parts of the Flos Aureus strand: Part I Foundations (fa_00..fa_03) Part II Expansion (fa_04..fa_07) Part III Crystal (fa_08..fa_09) Part IV Synthesis (fa_10) Part V Sacred Geometry (fa_11..fa_19) Part VI Physics Foundation (fa_20..fa_24) Part VII Algebraic Proofs (fa_25..fa_29) Part VIII Imagery & Genealogy (fa_30..fa_33) Two distinct header palettes: - Flos Aureus (yellow!4 / yellow!50!brown) for fa_NN: title carries petal name (e.g. 'Flos Aureus FA.05 Golden Bridge'), motif, Part, Lane, theorem count, Coq link, notation key. - Trinity S^3AI Strand (blue!3 / blue!40!black) for ch_NN: title carries chapter number, anchor, lane S<n>, theorem count, Coq link. Fields present in both palettes: anchor phi^2+phi^-2=3 (Trinity Identity, INV-22) + INV-k cross-reference via \citetheorem (task 1.6). Coverage: Patched: 68 chapters (34 fa_NN + 34 ch_NN with NN in 01..34) Skipped (bespoke pre-existing): ch_00, ch_35_mesh_node — left intact per R6 lane discipline. Total with Chapter Anchor: 70/70 = 100% coverage. Cross-check vs task 1.5/1.6 invariants (post amend): - Total \label sites: 1158 (unchanged) - Duplicate keys: 0 - Dangling refs: 0 - 119/119 referenced keys preserved New file: docs/phd/chapter-headers-audit.md (142 lines) — Flos Aureus manifest table + Trinity strand table + per-chapter audit with file/lane/petal/motif/theorem-count/header-presence. Stacked on feat/phd-phase1-unify-1-6 (PR #603). Skill: phd-chapter-author v1.1 + phd-monograph-auditor v1.2. Anchor: phi^2 + phi^-2 = 3, DOI 10.5281/zenodo.19227877. R1 (no .py/.sh committed). R5 (honesty): theorem counts mechanical; stub chapters honestly report 0; chapters without dedicated .v use per-theorem fallback link. R6 (lane discipline): no chapter prose touched; only header injection. R10 (atomic): one amended commit. * feat(phd-phase2-stubkill-2-8): expand App.H Zenodo DOI registry — Rust verifier (R1 fix), licence matrix, chapter↔DOI bridge, SHA cross-link, longevity policy [agent=phase2-2-8] - Pre-patch: 4,607 B / 127 lines, sections H.1..H.4 - Post-patch: 12,263 B / 259 lines, sections H.1..H.9 (+166% bytes, +132 lines) R1 violation fix: - Removed #!/bin/bash 'verify_dois.sh' block from §H.2 - Replaced with pointer to Rust subcommand cargo run -p trios-phd -- verify-dois (binary at crates/trios-phd/src/bin/verify_dois.rs; canonical DOI list at docs/phd/zenodo_dois.toml) R5-honest audit log: - §H.2 records sampled HTTP-200 verifications for 6 of the 13 DOIs (Z-01, Z-03, Z-04, Z-08, Z-13 plus historical training-run DOI 10.5281/zenodo.18947017), CONFIRMED 2026-05-08T23:55Z - Remaining 7 DOIs flagged for confirmation by the Rust audit binary at Phase 5 freeze (T-5); honest 'audit-pending' status, not fabricated PASS New sections: - §H.5 Per-artefact licence matrix (13 rows: CC-BY-4.0 / CC-BY-NC-ND-4.0 / MIT, by artefact kind) - §H.6 Chapter ↔ DOI cross-reference (13 rows; binding contract per R5) - §H.7 SHA-256 lock-file cross-link to AP.G §G.6.bis (the bridge between Zenodo deposits and the reproducibility.lock.json schema landed in PR #608's AP.G §G.6.bis) - §H.8 Longevity & migration policy (Zenodo primary + GitHub tag secondary + Software Heritage tertiary mirror; recovery procedure) - §H.9 Reviewer-2 mitigation (back-dating challenge → Z-13 pre-registration hash anchor; silent-amendment challenge → Zenodo DOI immutability + lock-file SHA check) Cross-reference audit (re-run): - 1158 \\label sites preserved (Phase 1 baseline) - 0 duplicates, 0 dangling refs - New \\ref{app:data-availability} resolves to AP.G line 14 - 17 begin/end pairs balanced Phase 2 STUB-KILL exit criterion: ≥8KB met (12,263 B). Phase 2 progress after this lane: 7/10 tasks done. Anchor: phi^2 + phi^-2 = 3 - Zenodo DOI 10.5281/zenodo.19227877 - defense 2026-06-15. Author: Dmitrii Vasilev <raoffonom@icloud.com> (ORCID 0009-0008-4294-6159) Skill: phd-monograph-auditor v1.2 + phd-chapter-author v1.1 + autonomous-research-loop Issue: #380 (Phase 2 task 2.8) Claim: #380 (comment) * feat(phd-phase2-stubkill-2-10): expand App.J Troubleshooting — STROBE overview, BLK↔chapter/Coq/Zenodo bridge, lessons learned, reproduction protocol, audit-pending log, R7 falsification hooks [agent=phase2-2-10] (#612)
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Closes #265\n\n## Phase 1 UNIFY · task 1.6 —
\citetheorem{INV-k}resolution through AP.FCloses part of trios#380 (task 1.6). Stacked on #602 (task 1.5) → #595 (task 1.2).
Problem
Chapters cite Coq invariants
INV-kas bare text.\citetheoremexisted only as a slide-only stub indefense/slides.texandappendix/F-coq-citation-map.texcarried no\label{thm:INV-k}anchors — body↔appendix-F cross-refs were dead text.Fix
Define
\citetheorem{INV-k}as a\providecommandinmain.texandmain_ru.texthat hyperrefs into appendix F:Add
\label{thm:INV-N}to every row of the INV summary table in F. The original table had 8 entries; appended 5 new rows for INV-{6, 9, 13, 22, 23} which are mentioned in chapter bodies.Why
\providecommand?defense/slides.texalready has a\newcommand{\citetheorem}[1]{[\textsc{#1}]}stub used when slides compile standalone.\providecommandinmain.texis non-overriding: when slides.tex is included in the full build, its stub stays active, but the macro is now also available corpus-wide for full-monograph builds.Inventory (post-patch)
INV-Nmentioned in body+appendix\label{thm:INV-N}in appendix F\labelsites (corpus)\refHonesty (R5)
INV-{9, 13, 22, 23} are mentioned in chapters but not yet primary records in
assertions/igla_assertions.json. Their rows in appendix F use\emph{registry-only}for theorem name and—for status, with\emph{no .v anchor}in the file column. This is explicit per R5 — the macro resolves to a hyperlink, but the appendix row signals registry status honestly.INV-6 is in JSON as
Proven(ema_decay_valid) — its row is canonical.Files changed
docs/phd/main.tex\citetheoremdefinitiondocs/phd/main_ru.texdocs/phd/appendix/F-coq-citation-map.tex\label{thm:INV-k}(8 inline + 5 new rows)docs/phd/citetheorem-map.mdAcceptance (per #380 task 1.6)
\citetheoremmacro defined corpus-widemain.tex+main_ru.tex\hyperref[thm:#1]defense/slides.texstub\providecommandformdocs/phd/citetheorem-map.mdSkill provenance & rules
phd-chapter-authorv1.1 +phd-monograph-auditorv1.2.py/.sh): patch script ran from/tmp/, only LaTeX + Markdown committed81db0d7for the macro + label additionsStacking note
Base of this PR is
feat/phd-phase1-unify-1-5(#602). After #595 → #602 → this lands, GitHub auto-rebases.🤖 Generated by
phd-chapter-authorskill v1.1 — Phase 1 UNIFY worker.Author: Dmitrii Vasilev
<raoffonom@icloud.com>— ORCID 0009-0008-4294-6159.