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SC-26: residual memory/divisibility scope (SC-16 / SC-3 classes) in the companions and the book - #959
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…ss companions and book Narrows the remaining sites that stated P-indivisibility, backflow or a Bell mechanism beyond what Main proves, each to the strongest proved statement: - Structure (abstract, :31, :90, :513, :752, :836, :903, :1025, :1306): the third audit feature is memory/divisibility; the memory mechanism transports, P-indivisibility is not established cross-framework (§14.3, §14.5 are the anchors). - Complexity §7.3/§7.6/§8.7-§8.9: readback lemma as a lower bound; protein application rests on the §7.2 model-independent consequence; memory-bearing design; backflow conditional on revival of distinguishability; NV figure marked heuristic. - Bioinformatics :138: ceiling attributed to the hidden-memory theorem and predictive-quotient fiber freedom; the GRN-in-fibers question open. - Main :131 (non-permutation T, C1 at first step), :620 (Bell checks C1 on the adopted branch), :696 (memory effects certify (ii)), :730 ledger row ((i) under (T) is universal). - SM :112, GR :591: recurrence-cycle P-indivisibility with its hypotheses. - Computation :83 / ch12 :232: memory witness vs Markov model. - Book: preface :3, ch01 :93/:207, ch02 :212, ch03 :36/:102/:114/:238/:240, ch13 :80, ch15 cluster (revival conditional on backflow), ch18 :193, appendix-c :14, README :76/:100; FULL mirrored. Explainer :135/:684/ :1005/:1033. SC-22, SC-23, SC-17, SC-19, SC-24, SC-25 sites untouched. Regenerated .tex/.pdf for the eight papers and the book. Bands unchanged. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y87wExth9RoUb3dtbumhTb
Required findings, each verified against the source:
1. NV and coherence numbers removed where the corpus's own anchors say no
factor is derived (ch15 :104, :134; appendix-a F3/F4; Complexity table):
ch15 :18, :130, :132, :244, §15.9 item 2; Complexity :488, :490.
2. Complexity :484: memory cases vs revival cases, each with its source.
3. ch15 :116, :128: accessible conditional memory first, revival a further
signature; :18, :122 "predicts" -> "proposes" for backflow-conditioned
claims.
4. GR :591: the recurrence argument on a finite invariant constraint surface
with per-fiber hidden prior (finite order, K_L = I, stochastic-inverse
lemma), stated as a one-line argument; full-support prior removed; (C1)
grounded in Main §1.3's ADM/constraint coupling, not in data correlation.
5. ch01 :163: conditional memory identifies the memory-bearing sector.
6. SM :112: site two-slice partition; the update adds the uniform hidden
x_{L-1}(t), so the one-step map is not a permutation (L >= 4, q >= 2).
7. Main :730: label restating and history voice removed.
8. preface :3 and ch03 :36/:102/:114/:240: finite reversible hypothesis and
the memory/divisibility feature name.
Optional 9-14: Bioinformatics :138 and ch17 :14 stated as the conditional
theorem; Explainer :135; Complexity :370; ch15 :138; Structure :903, :1041.
Rebuilt the seven papers and the book. Bands unchanged.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Y87wExth9RoUb3dtbumhTb
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…to their current heads Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y87wExth9RoUb3dtbumhTb
Same-document contradictions beside the conditional text, each verified:
1. Bioinformatics :18, :48, :142, (P4) :148, (P6) :152, (P7) :198, :459,
:463, :465, :467, :469: the transcriptome ceiling stated as the
conditional theorem of :138; whether a quantity lies in the hidden
fibers is open.
2. ch17 :14, :20, :30, :34, :36, :40, :42, :70, :72, (P1) :218, :206: the
strict gap I(phenotype|T) < I(phenotype|T,S) as the framework's
hypothesis, open per task.
3. ch15 :16, :49, :87, :134, :260: error-correction, sensing and overhead
magnitudes removed (anchors: §15.9 item 1, appendix-a F2, Complexity
:486/:496).
4. ch03 :36, :102, :114, :240: memory/divisibility as accessible memory
where the hidden sector reads back its record (C4), and recurrence-cycle
P-indivisibility on finite reversible substrata (Structure :1025).
Optional: GR :591 finite representative; K_{mL} = I for the s >= L case.
Rebuilt Bioinformatics, GR and the book. Bands unchanged.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Y87wExth9RoUb3dtbumhTb
- Bioinformatics :56, :186; ch17 :12, :22, :78, :210 (+FULL): the ceiling and its explanatory reading stated conditionally; ch17 :78's uncomputed "structurally calculable amount" stated as not computed. - ch15 :134 (+FULL): SQUID comparison deleted, per the owner's ruling on counterfactual performance comparisons. - Optional: ch15 :91 factor-of-three target removed; ch17 :76 "outperform transcriptome-only methods"; GR :591 "m >= 0". Rebuilt Bioinformatics, GR and the book. Bands unchanged. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y87wExth9RoUb3dtbumhTb
Reconciles #959 with main after #958. The .md and verification/ merges were clean. The only conflicts were generated files: Main, GR, SM and the book .tex/.pdf, regenerated from the merged sources with sh ./build.sh (page counts unchanged; every source-sha256 stamp matches). The landing against the new main is exactly this branch's own .md and verification/ diff, so nothing of #958 is reverted. Release gate: every step passes except lean-axioms (no lake locally); edge_rigidity_probe passes. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y87wExth9RoUb3dtbumhTb
The optional nit from the final confirmation at e71371d: the summary at ch17 :26 now reads "a conditional structural ceiling (… where the strict gap holds)", matching :12, :14 and §17.2. Book regenerated. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y87wExth9RoUb3dtbumhTb
Reconciles #959 with main after #956. The .md merges were clean, including Complexity and Explainer, where the two PRs edit different lines. The only conflicts were generated files (Complexity, Explainer and the book .tex/.pdf), regenerated from the merged sources with sh ./build.sh. Every source-sha256 stamp matches. Against the new main, the landing is exactly this branch's own diff over 4449b0d (file set and line set), so nothing of #956 is reverted. Release gate: every step passes except lean-axioms (no lake locally); edge_rigidity_probe passes. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y87wExth9RoUb3dtbumhTb
Reconciles #959 with main after #957. The .md and verification/ merges were clean: in SM and Main the two PRs edit different lines. The only conflicts were generated files (Main, SM and the book .tex/.pdf), regenerated from the merged sources with sh ./build.sh. Every source-sha256 stamp matches. Against the new main, the landing is exactly this branch's own diff over f92279a (file set and line set), so nothing of #957 is reverted. Release gate: every step passes except lean-axioms (no lake locally); edge_rigidity_probe passes. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y87wExth9RoUb3dtbumhTb
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…; #957 main CI green Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y87wExth9RoUb3dtbumhTb
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…records of #959 and #961-#968 CORRECTIONS-LEDGER.md records, per unit, the original flaw, the corrected claim, the evidence level, the affected manuscripts, the verification artifacts and the merge status (owner request). The review records are saved verbatim from the reviewers' reports. Local filesystem paths are redacted to repo-relative paths in 957-REVIEW-b25dcfc4.md, and two uncommitted reviewer scratch scripts in matrix/part-B4.md are named without their scratch paths. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y87wExth9RoUb3dtbumhTb
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…udit) Brings in SC-24 to SC-27 (#956-#959). Clean automatic merge; LEDGER.json auto-merged with both sides' rows. Release gate passes locally except lean-axioms (CI). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Y87wExth9RoUb3dtbumhTb
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Source-correction unit SC-26 of the #942 audit (gate #946). Base:
main55e3217b, the merged #955 tree. Head:64c20e7e.Review history:
7c1178278d8ca8c672eece1164c20e7emainhas moved. It is now at4449b0d9, after #958 (SC-27) merged. A test merge resolves every.mdautomatically. Only generated.tex/.pdfconflict: Main, GR, SM and the FULL book. Reconciliation (mergemain, regenerate withsh ./build.sh, then check that the landing equals this PR's own diff) is pending a decision on timing, because it moves the head.Each residual site that stated P-indivisibility, backflow, a Bell mechanism, a numerical gain or an unconditional ceiling beyond what the corpus proves now states the strongest proved result. Three notions are kept apart:
Sites
No change, with reasons:
Excluded, belonging to other units:
Findings 4 and 6
GR :591, option (a): the argument is stated in the text.
isPermMatrix_of_stochastic_inverse).The re-review confirmed the argument.
SM :112.
python3 -I -B, not committed) covered (4,2), (4,3) and (5,2). In each case φ is a bijection, T is not a permutation, and the rows are uniform.26d5fb4a…; output sha256511ff827….Checks (at
64c20e7e)sh ./build.shsucceeds for every touched paper and for--book, with no dropped glyphs.lean-axioms, which needslakeand is absent locally. Coverage is OK at 128 statements, with no fingerprint changed.mirrorreports 0 lines absent, andclaimspasses.edge_rigidity_probe.pyreports ALL CHECKS PASS.Correctness bands unchanged: every edit narrows a claim to its proved scope, and SM :112 states a property proved for the stated partition.
Links: #942, #946.
🤖 Generated with Claude Code
https://claude.ai/code/session_01Y87wExth9RoUb3dtbumhTb