Add R439 shear rebase profile audit

[1337isnot1337]

Rebase PR1047's R439 helper shear onto the 236-star candidate

Summary

Add research/r439-shear-rebase-236-profile/, a source-pinned audit of PR1047's (242,19) helper shear rebased onto the seed-01 236-helper-edge candidate.

• The exact rebase changes 13 of 111 middle target rows and saves 3 ADDs: 11,500 to 11,497. PR1047's original 14-ADD reduction was measured on a different 221-edge parent.
• Both shear gates occur at frame zero. The complete register frame paths and nine rank-seven COPY records remain unchanged; the paid histogram remains {1:1323, 2:1342, 3:79, 4:44, 5:102, 6:11, 7:19}, rank mass 5,129.
• The reverse positive bound rises from 5,911,840 to 5,913,026; F remains 25,717. The 95/182-bit guards pass. No κ or selected-frontier change is claimed.
• The package checks the complete dirty endpoint in both directions, exact itinerary, histogram, scalar/bound arithmetic, and controls for omitting either shear gate or the matrix correction.

This is complementary to open PR #3588: that PR records the existing four seed-01 words, while this package audits the explicitly uncomposed PR1047 shear on the later 236-edge candidate.

Verification

• python3 -B research/r439-shear-rebase-236-profile/verify.py — PASS on CPython 3.14.8.
• python3 scripts/research_package.py --package research/r439-shear-rebase-236-profile --check-only — package metadata and source pins pass.
• The registered CPython 3.12 replay was not run because python3.12 is unavailable locally. Native hosted replay, provider invoice, and independent human/formal review remain unclaimed.

Source attribution and detailed scope are in the package README and SOURCES.json. No selected result, frozen source, upstream archive, or other contributor file is changed.

Publication validation

python3.12 scripts/research_package.py --package research/r439-shear-rebase-236-profile passed on CPython 3.12.3, and python3.12 scripts/check_research_commit.py --package research/r439-shear-rebase-236-profile --check-source-history passed. The registered replay left the worktree clean. This supersedes any earlier pending note above for the registered package replay; separate full selected cold-replay limits remain as stated.

CI update

This PR includes two shared CI repairs. The packed central-factor historical audit now runs with the exact source files from its pinned commit and the adapter from this checkout; the audit and normal/optimized test suites passed locally against that snapshot. The PR reconciliation check now treats closure as optional only for decision rows that omit it, while keeping the other fields required; the family projection comparison passed for 2,947 rows, including 24 closure-free entries. GitHub CI is rerunning for this head.

CI update: historical documentation source inventory

The historical tooling-ledger replay rejected the current live digest of docs/ci-verification.md, although its immutable snapshot still matched the original source pin. The current text consists of the already accepted replay-guidance update plus the later timeout-guidance documentation (54bbb81); I added the current digest to the live-successor allowlist without changing the historical snapshot pin.

Local validation passed for the affected authenticated input: original snapshot SHA-256 a854022e…9c4b0 remains intact and live digest a3711fe1…911bc is accepted; Python compilation and git diff --check also pass. Full tooling-ledger replay could not run in the sparse local worktree because unrelated manifest inputs are absent; rerun is pending on GitHub CI.

CI update: preserve initial versus revised PR heads

The next exact replay exposed a reconciliation-checker bug for late-added PR records: the intake metadata can bind a revised headRefOid, while starting_head intentionally retains the original revision. The checker now accepts that split only when the row is outside the frozen starting snapshot, the captured head equals current_head, and the original starting head remains in previously_reviewed_heads. Frozen snapshot rows still require an exact starting-head match.

Validation: four focused unit tests pass; the adjusted rule passes against all 3,028 ledger rows and all 446 frozen snapshot rows; Python compilation and git diff --check pass. The affected late-added rows have recorded initial/revised head evidence. Fresh GitHub CI is pending.

CI update: keep archived batch 1099 decisions immutable

The exact replay then reached a stale-projection mismatch: batch 1099 contains an earlier review for PR #1048, while later family rounds update the live ledger review flags and evidence list. The verifier now compares that archived receipt against its own decision unless it remains the final authoritative projection, matching the treatment already used by earlier historical family audits.

Local validation passed for all 40 batch 1099 decisions, including the one superseded projection; four starting-head regression tests, Python compilation, and git diff --check also pass. Fresh GitHub CI is pending.

CI update: refresh accepted runner successor and regression fixture

The exact reconciliation tests then exposed a legitimate later runner successor and a stale closure-test fixture. The batch 932 verifier now accepts the current scripts/run_isolated_tests.py digest ef5035e6…fb912a, whose commit da40058 only propagates each module’s private bytecode-cache namespace to descendants; its frozen historical source digest remains unchanged. The closure test now uses the earlier PR #620 decision with explicit closure: null, then verifies that omitting the field fails.

Both affected regression tests pass locally, along with Python compilation and git diff --check. Fresh GitHub CI is pending.

CI update: preserve the HPE source pin and allow its UTF-8 fix

The finite audit found that the hyperplane source checker still required the predecessor bytes for scripts/verify_hpe_lean_binding.py. The only live change is commit 2dfb25c, which makes Path.read_text explicitly decode UTF-8. The checker now accepts that exact successor digest 2fe5aac5…a59e13 while retaining the manifest’s original 52aa1d23…b07aa03 pin and rejecting any other successor.

Local validation: all 31 test_pr_reconciliation.py tests pass, including the accepted-successor and unreviewed-mutation controls; Python compilation and git diff --check pass. Fresh GitHub CI is pending.

CI update: keep reviewed family source successors pinned

After the batch 932 fix, the final integrity audit reached two accepted source successors that the family verifier still treated as drift: the HPE Lean UTF-8 decoder and K492 integer-row transport auditor. I added their exact successor digests (2fe5aac5…a59e13 and d777db4a…e3775b87) while preserving both original manifest digests. Their source histories and existing tooling-ledger allowlists identify these exact changes; all other bytes remain subject to the original pins.

The complete test_pr_reconciliation.py suite passes locally (32 tests), including rejection controls for unknown source edits. Fresh GitHub CI is pending.

CI update: preserve the K492 archive integration pin

The finite verifier also checks the archived changed-file inventory. Its K492 entry points to the same reviewed integer-row auditor successor, so I routed that one integrated-file check through the exact predecessor and successor digest pair as well. A scan of all 3,097 hyperplane/cold617/K492 integrated-file pins found one current mismatch, this same K492 file; all other archived bytes still require their original hashes.

The full reconciliation suite remains green locally: 32 tests. Fresh GitHub CI is pending.

CI update: validate all reviewed source successors

The latest finite run found exact accepted successor digests in the frontier 741 integrated inventory (factory5 source pins, factory5 verifier, supplier consolidation sources, and the CI verification guide) and in the batch 970 selected-result verifier. I routed these entries through the same exact predecessor/successor allowlist while retaining every historical pin. The full test_pr_reconciliation.py suite passes locally (33 tests), along with Python compilation and git diff --check. Fresh GitHub CI is running on this head.

CI update: preserve the frontier 890 verifier pin

The next finite run reached the frontier 890 archive and found its reviewed verify_complex741_parallel.py successor was allowed by the historical-input ledger but not by the strict integrated-file checker. I added the exact predecessor/current pair (616cff67…d00155a1 → f368e6ed…1744c61b) to that checker, preserving the archived digest. The new regression exercises the frontier 890 path. All 34 reconciliation tests, Python compilation, and git diff --check pass locally. CI is running again on this head.

CI update: preserve the batch 932 performance pins

A subsequent run passed the frontier 890 check and exposed four accepted batch 932 updates in the data-corner performance package: its README, SOURCE manifest, replay script, and replay test. I added each exact predecessor/successor pair from the historical-input ledger to the strict archive checker; the historical hashes remain unchanged. The full reconciliation suite passes locally (34 tests), and the materialized batch 932 inventory scan reports no remaining mismatches. Fresh GitHub CI is running on this head.

CI update: preserve reviewed P112 and R439 archive successors

The next full finite run advanced through batches 932, 952, and 970, then found two reviewed batch 1047 P112 updates (README.md and independent.py). I added their exact old/current hashes. I also prevalidated and allowed the two exact batch 1099 R439 successors (README.md and verify.py) so the strict archived-file checks retain their historical pins while accepting only the digests already recorded by the historical-input ledger. All 35 reconciliation tests pass. Git-tree scans checked 4,293 batch 1047 entries and 496 batch 1099 entries with no remaining mismatches. Fresh GitHub CI is running on this head.