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feat(phd-phase2-stubkill-2-6): expand AP.G Data Availability — INV-1..15 catalogue, falsification witnesses, INV-7 pre-reg, AVL/INV bridge#608

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feat(phd-phase2-stubkill-2-6): expand AP.G Data Availability — INV-1..15 catalogue, falsification witnesses, INV-7 pre-reg, AVL/INV bridge#608
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@gHashTag gHashTag commented May 8, 2026

Closes #265\n\n# Phase 2 STUB-KILL · task 2.6 — AP.G Data Availability expansion

Anchor: φ² + φ⁻² = 3 · DOI 10.5281/zenodo.19227877 · defense 2026-06-15
Issue: trios#380 Phase 2 task 2.6
Claim: #380 comment 4408253407
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
Stack: stacked on #605#603#602#595main

TL;DR

Phase 2 STUB-KILL task 2.6 satisfied: docs/phd/appendix/G-data-availability.tex expanded from 6,662 B / 152 lines18,560 B / 342 lines (+178%, well over the ≥8 KB Phase 2 exit criterion). All 13 Coq invariants from assertions/igla_assertions.json are now catalogued in AP.G, with falsification witnesses, INV-7 pre-registration block, honest-Admitted budget breakdown, and an explicit Appendix F ↔ JSON-registry bridge.

What changed

R5-honest namespace separation

The pre-patch AP.G used INV-1..INV-7 for reproducibility checks (SHA / grep / DOI resolution); Appendix F uses INV-1..INV-13 for Coq theorems. The two semantics collided. This PR resolves the collision by:

  1. Renaming AP.G's local invariants INV-N → AVL-N (Available-data invariants)
  2. Inserting a clarifying note at the top of §G.3 explicitly stating the two namespaces are disjoint
  3. Adding §G.10 as an explicit bridge between the two registries

R5: zero theorem statuses were flipped during the rename.

New sections (4 new + 1 sub-section)

Section Source Content
§G.6.bis Per-invariant SHA-256 ledger reproducibility.lock.json ACM AE Reusable badge schema (5 columns)
§G.7 Coq Invariant Catalogue (INV-1..INV-15) assertions/igla_assertions.json invariants[] 13 rows verbatim
§G.7 Honest-Admitted budget paragraph _metadata.admitted_budget 3 file-level entries, 5 theorems total (lr_phi_optimality.v 3, lucas_closure_gf16.v 1, igla_found_criterion.v 1)
§G.8 Falsification witnesses per invariant _metadata.falsification_witnesses 7 INV-N witnesses verbatim
§G.9 INV-7 pre-registration block (anti-HARKing seal) _metadata.preregistration["INV-7"] full hypothesis (BPB<1.50, ≥3 distinct seeds, post-warmup, finite, Welch-t α=0.01 vs μ₀=1.55), 7 refuting conditions
§G.10 Appendix F ↔ JSON-registry cross-reference manual bridge 16 rows: 13 F-listed + 3 JSON-only wip rows (INV-6-HybridQkGain, INV-14, INV-15)

Acceptance numbers

total_label_sites: 1158       ← preserved from Phase 1 baseline
unique_keys      : 1158       ← 0 duplicates
dangling_refs    : 0          ← clean
pre_refs_count   : 119        ← preserved
post_refs_dangling: 0
post_refs_resolved: 119

\begin/\end balance: 17 pairs balanced
File size before: 6,662 B
File size after : 18,560 B  (+11,898 B, +178%)
Lines  before:    152
Lines  after :    342  (+190)
Sections before:  6
Sections after :  10 + 1 sub-section  (+4 + 1 sub)

The new \ref{app:F}, \ref{app:falsification}, \ref{app:acm-ae} all resolve to existing \label{} sites.

R-rule compliance

  • R1 (Rust/Zig only): patch is .tex-only, no .py/.sh shipped to repo.
  • R5 (Honest Admitted vs Proven): every row in §G.7 carries Proven/Admitted/wip exactly as the JSON registry records. Zero flips.
  • R6 (Zero free parameters): every numeric constant traces — α=0.01, μ₀=1.55, BPB=2.2393, BPB<1.50, sanctioned seeds {F₁₇=1597, F₁₈=2584, F₁₉=4181, F₂₀=6765, F₂₁=10946, L₇=29, L₈=47}, all from assertions/igla_assertions.json.
  • R7 (Falsification): §G.8 lists 7 falsification witnesses; §G.9 carries the INV-7 pre-registration; §G.10 cross-refs Appendix B.
  • R10 (Atomic commits): single commit bf8a968.
  • R13 (ACM AE badges): §G.6.bis schema explicitly addresses Reusable badge requirements; §G.7 / §G.8 / §G.9 strengthen Functional + Available.
  • R14 (Coq citation map): every theorem in §G.7 traces to a .v file path verbatim from JSON; §G.10 is the explicit bridge to Appendix F.

Phase 2 STUB-KILL progress after this lane

# Task State
2.1 AP.B 4 Popper falsifier-clauses done in prior session (Doctor Update 2026-05-04)
2.2 AP.B φ-claim ↔ non-φ control pairs done in prior session
2.3 AP.C ≥8KB w/ GF4/8/16 tables DONE pre-existing (9,305 B)
2.4 AP.D Trinity↔Flos Aureus symmetry table DONE pre-existing (6,246 B; symmetry table + §D.2 proof)
2.5 AP.E Lexicon constants deferred to Neon SSOT
2.6 AP.G INV-1..7 + Zenodo DOIs THIS PR ✅ 18,560 B
2.7 App.F FPGA bitstream + SHA-256 open (4,932 B → ≥8 KB target)
2.8 App.H 13 Zenodo DOI registry open (4,607 B)
2.9 App.I XDC pin map open (4,435 B)
2.10 App.J Troubleshooting open (6,100 B)

After this lane lands: 6/10 tasks of Phase 2 functionally complete.

Files

  • docs/phd/appendix/G-data-availability.tex — expanded (+11,898 B; preserves all §G.1–G.6 content verbatim except namespace rename INV→AVL)
  • docs/phd/appendix-G-expansion-audit.md — 102-line audit with line-by-line diff log

Anchor

φ² + φ⁻² = 3 · DOI 10.5281/zenodo.19227877

….15 catalogue, falsification witnesses, INV-7 pre-reg, AVL/INV bridge [agent=phase2-2-6]

- 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)
@gHashTag gHashTag merged commit d73d2f2 into feat/phd-phase1-unify-1-4 May 10, 2026
9 checks passed
@gHashTag gHashTag deleted the feat/phd-phase2-stubkill-2-6 branch May 10, 2026 20:50
gHashTag added a commit that referenced this pull request May 10, 2026
….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)
gHashTag added a commit that referenced this pull request May 10, 2026
…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)
gHashTag added a commit that referenced this pull request May 10, 2026
…t 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)
gHashTag added a commit that referenced this pull request May 10, 2026
…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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