feat(phd-phase2-stubkill-2-10): expand App.J Troubleshooting — STROBE / cross-link / R7 hooks#612
Merged
gHashTag merged 1 commit intoMay 10, 2026
Conversation
… overview, BLK↔chapter/Coq/Zenodo bridge, lessons learned, reproduction protocol, audit-pending log, R7 falsification hooks [agent=phase2-2-10]
gHashTag
added a commit
that referenced
this pull request
May 10, 2026
… overview, BLK↔chapter/Coq/Zenodo bridge, lessons learned, reproduction protocol, audit-pending log, R7 falsification hooks [agent=phase2-2-10] (#612)
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)
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Closes #265\n\n## Phase 2 STUB-KILL · task 2.10 — App.J Troubleshooting expansion
Closes trios#380 Phase 2 manifest task 2.10 (line 67).
Pre/post
docs/phd/appendix/J-troubleshooting.tex\labelsites in J\labelsites\begin/\endenv balanceWhat changed
ch_20:abstract), Zenodo Z-08 (10.5281/zenodo.19227884), with 3/5 entries honestly markedaudit-pending(R5)cargo run -p trinity-fpga -- bringup(R1: no.sh/.py), idempotent, gated bytrinity_fpga::bringup::idempotentintegration testPreserved verbatim
R-rule compliance
.py/.shblocks; reproduction usescargo run -p trinity-fpga -- bringupaudit-pendingrather than asserted0066a58Stack
feat/phd-phase2-stubkill-2-8(PR #609, tipcf3033c)feat/phd-phase2-stubkill-2-10tip0066a58🌻 Phase 2 STUB-KILL: 8/10 lanes done after this merge.
φ² + φ⁻² = 3 · DOI 10.5281/zenodo.19227877 · defense 2026-06-15