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Overnight Maintenance Log - 2026-07-04

Branch: codex/overnight-maintenance Upstream: origin/codex/overnight-maintenance Spec: external overnight-maintenance/maintenance-spec.md skill spec Parameters: PASSES=20, MAX_PASSES=50, PUSH=yes, NUMBERED_DOCS=yes

1. Coverage Decisions

Applied checks: - Baseline repository scan: Python code, notebooks, tests, docs, scripts, CI, Docker, devcontainer, dependency manifests. - Documentation indexing and hierarchical numbering because NUMBERED_DOCS=yes. - End-to-end execution-flow tracing for notebooks, scripts, Makefile targets, generated docs, and verifier entry points. - Documentation-surface review for README, MkDocs, repository metadata, and the project wiki/Pages state. - Error-handling, configuration, secrets, versioning, build, supply-chain, complexity, dependency-contract, and examples/library-fit checks.

Skipped checks: - HTTP/RPC handler contracts: N/A, no service handlers found in this repository. - Database and migration hygiene: N/A, no persistent database or migration files found. - i18n/a11y UI checks: N/A, no user-facing frontend application found. - Multi-language parity for active surfaces: N/A for active notebooks and Python helpers; archived CodexGLUE material is reviewed as archive hygiene, not an active supported surface. - Performance budget benchmarking: N/A unless a repository-declared performance budget is found during pass review.

2. Pass History

Pass Type Issues Coverage Evidence Result
1 genuine 12 Fresh-eyes report-only subagents reviewed active notebooks/examples, published docs surfaces, tooling/security/reproducibility, and complexity/tests; local fixes covered orphaned notebook-reorganization records, nested-doc verifier coverage, subprocess timeout defaults, PyG runtime canary accuracy, NNx editable-install contract boundaries, and genai-vanilla submodule contract ledgering. Validation: focused red/green verifier tests; python scripts/verify_repo.py --check all --fast (0 errors, 4 warnings); make docs-build; ruff check . --no-cache; pytest tests/ -v (381 passed, 3 skipped, 17 warnings); make check-tier-a-clean; shellcheck scripts/start-jupyterhub.sh; python -m py_compile scripts/verify_repo.py; git diff --check. Non-zero pass; fixes applied; zero-issue streak reset; remaining notebook/API-fit, output-hash, Pages, CI-signal, and dependency-refresh items deferred with rationale
2 genuine 11 Fresh report-only subagents reviewed notebooks/examples, docs/published surfaces, tooling/security/reproducibility, and complexity/tests against the current tree; local trace covered .github/workflows/*, Makefile papermill targets, docs/index.md, docs/dependency-contracts.md, docs/FINDINGS-NNX.md, docs/diagrams/*, NumPy notebook helper modules, verifier constants, and live repository metadata. Validation: red/green pytest tests/test_numpy_layers.py -v; pytest tests/test_numpy_layers.py tests/test_verify_repo.py -q (60 passed); workflow YAML parse; python scripts/verify_repo.py --check docs --fast (0 findings); ruff check . --no-cache; python -m py_compile scripts/verify_repo.py; python scripts/verify_repo.py --check all --fast (0 errors, 4 known warnings); make docs-build; pytest tests/ -v (384 passed, 3 skipped, 17 warnings); make check-tier-a-clean; shellcheck scripts/start-jupyterhub.sh; pip-audit -r requirements.txt -r torch-requirements.txt (23 known vulnerabilities, ledgered); git diff --check. Non-zero pass; fixes applied for docs surfacing, tooling timeouts, action pins, NumPy layer validation, and stale docs wording; zero-issue streak reset; live Pages, notebook modernization, output hashing, dependency lockfiles, and complexity refactors remain deferred
3 genuine 3 Fresh report-only subagents reviewed active notebooks/examples, docs/diagrams/published surfaces, tooling/security/dependency contracts, and Python code/tests/complexity; local trace covered active notebook papermill metadata, README library-fit wording, genai-vanilla pinned and upstream contracts, GitHub Actions pins, live Pages/About metadata, tracked data/runs/cache artifacts, stale ml-lab references, and standard validation. Validation: red/green pytest tests/test_verify_repo.py::test_e14_flags_tmp_papermill_output_path -q; python scripts/verify_repo.py --check execution --fast (0 findings after cleanup); python scripts/verify_repo.py --check all --fast (0 errors, 4 known warnings); ruff check . --no-cache; make docs-build; pytest tests/ -v (385 passed, 3 skipped, 17 warnings); python -m py_compile scripts/verify_repo.py; shellcheck scripts/start-jupyterhub.sh; bash -n scripts/start-jupyterhub.sh; pip-audit -r requirements.txt -r torch-requirements.txt (23 known vulnerabilities, ledgered); notebook JSON parse; git diff --check. Non-zero pass; fixes applied for stale papermill metadata, stale README wording, and genai-vanilla upstream ledger drift; zero-issue streak reset
4 genuine 4 Fresh report-only subagents reviewed active notebooks/examples/archive placement, documentation/published surfaces, tooling/security/dependency contracts, and Python code/tests/complexity; local trace covered active/archive notebook inventory, relative ./data and ./runs references, papermill metadata, tracked data/runs/cache artifacts, stale ml-lab references, GitHub Actions pins, live Pages/About/wiki state, genai-vanilla submodule wording, Docker bootstrap ledger wording, Reddit phase-2 run selection, quantization facade coverage, and standard validation. Validation: red/green pytest tests/nnx_surface/test_notebook_api_surface.py::test_phase2_notebook4_ranks_local_runs_not_cross_experiment_registry -q; pytest tests/nnx_surface/test_quantization_mnist_ffnn_pytorch.py -q; notebook JSON parse for the Reddit phase-2 notebook. Non-zero pass; fixes applied for submodule/ledger wording, Reddit local-run ranking, stale Reddit outputs, and quantization facade coverage; zero-issue streak reset; live Pages/default-branch docs, NNDataset(batch_sizes=...) modernization, output hashing, CI signal, bootstrap lockfile pinning, and verifier complexity remain deferred
5 genuine 1 Fresh report-only subagents reviewed notebook artifacts/examples, docs/diagrams/published surfaces, tooling/security/dependency contracts, and Python code/tests/complexity; local trace covered branch/upstream parity, active/archive notebook inventory, papermill metadata, tracked data/runs/cache artifacts, stale ml-lab references, live Pages/About/wiki state, GitHub Actions pins, genai-vanilla upstream state, CI signal, and standard validation. Validation: python scripts/verify_repo.py --check all --fast (0 errors, 4 known warnings); pytest tests/ -v (389 passed, 3 skipped, 17 warnings); ruff check . --no-cache; make docs-build; make check-tier-a-clean; shellcheck scripts/start-jupyterhub.sh && bash -n scripts/start-jupyterhub.sh; python -m py_compile scripts/verify_repo.py; notebook JSON/metadata parse; git diff --check; pip-audit -r requirements.txt -r torch-requirements.txt (23 known vulnerabilities, ledgered). Non-zero pass; fixed fresh genai-vanilla upstream ledger drift; zero-issue streak reset
6 genuine 4 Fresh report-only subagents reviewed notebook artifacts/examples/archive hygiene, docs/diagrams/published surfaces, tooling/security/dependency contracts, and Python code/tests/complexity; local trace covered branch/upstream parity, active/archive notebook inventory, top-level papermill metadata, tracked data/runs/cache artifacts, stale ml-lab references, live Pages/About/wiki state, GitHub Actions pins, genai-vanilla pinned runtime content, CI signal, test subprocess timeout coverage, and standard validation. Validation: red/green pytest tests/test_verify_repo.py::test_e14_flags_source_notebook_papermill_metadata -q; focused changed tests (13 passed, 3 warnings); python scripts/verify_repo.py --check execution --fast (4 warnings before cleanup, 0 findings after); python scripts/verify_repo.py --check all --fast (0 errors, 4 known warnings); pytest tests/ -v (390 passed, 3 skipped, 17 warnings); ruff check . --no-cache; make docs-build; shellcheck scripts/start-jupyterhub.sh && bash -n scripts/start-jupyterhub.sh; python -m py_compile ...; notebook JSON/metadata parse; git diff --check; pip-audit ... (23 known vulnerabilities, ledgered). Non-zero pass; fixed stale active notebook papermill metadata, consumed the genai-vanilla runtime bump, narrowed wiki status, and added test subprocess timeouts; zero-issue streak reset
7 genuine 4 Fresh report-only subagents reviewed notebook/archive artifacts, docs/diagrams/published surfaces, tooling/security/dependency contracts, and Python code/tests/complexity; local trace covered branch/upstream parity, 51 notebook JSON parse, active/archive notebook paths, ignored data/runs/cache artifacts, stale runtime package references, live Pages/About/default-branch state, GitHub Actions pins, genai-vanilla pinned and upstream contracts, shell/YAML/script contracts, and standard validation. Validation: focused archive guard regression (1 passed); python scripts/verify_repo.py --check all --fast (0 errors, 4 known warnings); pytest tests/ -v (391 passed, 3 skipped, 17 warnings); ruff check . --no-cache; make docs-build; shellcheck scripts/start-jupyterhub.sh && bash -n scripts/start-jupyterhub.sh && sh -n vendor/genai-vanilla/start.sh && sh -n vendor/genai-vanilla/stop.sh; python -m py_compile ...; notebook JSON parse; git diff --check; pip-audit ... (23 known vulnerabilities, ledgered). Non-zero pass; consumed fresh genai-vanilla upstream bump, fixed stale runtime docs, guarded archive cross-language notebooks against missing historical artifacts, cleaned ignored duplicate local run/cache artifacts, and left live Pages/default-branch drift plus NNx facade-import modernization deferred; zero-issue streak reset
8 genuine 5 Fresh report-only subagents reviewed archive notebooks, docs/published surfaces, tooling/dependency contracts, and Python tests/complexity; local trace covered branch/upstream parity, 51 notebook JSON parse, git-tracked archive notebook discovery, CodeXGLUE cross-language and RoBERTa archive execution paths, genai-vanilla pinned and upstream contracts, live Pages/About/default-branch state, GitHub Actions branch signal, shell/script contracts, and standard validation. Validation: red/green RoBERTa archive opt-in guard; focused archive regressions (3 passed, 3 warnings); red/green test-double keyword-contract cleanup; python scripts/verify_repo.py --check all --fast (0 errors, 4 known warnings); ruff check . --no-cache; make docs-build; pytest tests/ -v (393 passed, 3 skipped, 17 warnings); shell/script syntax and lint; python -m py_compile ...; notebook JSON parse (51 parsed, 0 errors); git diff --check; make check-tier-a-clean; pip-audit ... (23 known vulnerabilities, ledgered). Non-zero pass; consumed fresh genai-vanilla upstream bump, made archived RoBERTa rebuilds explicit opt-in, tightened cross-language archive missing-artifact/timeouts, restricted archive helper tests to git-tracked notebooks, removed unused test parameters, and kept live Pages/default-branch drift plus NNx modernization deferred; zero-issue streak reset
9 genuine 4 Fresh report-only subagents reviewed active/archive notebooks, docs/published surfaces, tooling/security/dependency contracts, and Python code/tests/complexity; local trace covered branch/upstream parity, 51 notebook JSON parse, ignored docs/superpowers/ scratch status, CodeXGLUE RoBERTa default-run write paths, verifier S2 import extraction, live Pages/About/default-branch state, GitHub Actions branch signal, genai-vanilla pinned/upstream parity, shell/script contracts, and standard validation. Validation: red/green RoBERTa archive helper-copy/cwd guard; red/green S2 multi-import guard; focused affected tests (355 passed, 3 warnings); python scripts/verify_repo.py --check all --fast (0 errors, 4 known warnings); ruff check . --no-cache; make docs-build; pytest tests/ -v (394 passed, 3 skipped, 17 warnings); pip-audit ... (23 known vulnerabilities, ledgered); shell/script syntax and lint; python -m py_compile ...; notebook JSON parse (51 parsed, 0 errors); git diff --check; make check-tier-a-clean. Non-zero pass; fixed RoBERTa archive default write-on-run/cwd mutation, fixed verifier S2 multi-import blind spot, documented audit-baseline and NLP-asset integrity gaps as deferred, rejected ignored-local docs/superpowers/ stale links as non-repo scratch, and kept live Pages/default-branch drift plus NNx modernization deferred; zero-issue streak reset
10 genuine 2 Fresh report-only subagents reviewed active/archive notebooks, docs/published surfaces, tooling/security/dependency contracts, and Python code/tests/complexity; local trace covered branch/upstream parity, genai-vanilla upstream drift, 51 notebook JSON parse, RoBERTa archive guard state, verifier S2 AST/fallback behavior, live Pages/About/default-branch state, GitHub Actions branch signal, shell/script contracts, and standard validation. Validation: red/green S2 magic-plus-multi-import guard; git ls-remote found genai-vanilla d8ddd8e; pinned JupyterHub requirements/Dockerfile still contain thekaveh-nnx[lm]==0.2.0, notebook runtime deps, en_core_web_sm, and vader_lexicon; python scripts/verify_repo.py --check all --fast (0 errors, 4 known warnings); targeted S2 tests (2 passed); ruff check . --no-cache; make docs-build; shell/script syntax and lint; python -m py_compile ...; notebook JSON parse (51 parsed, 0 errors); git diff --check; make check-tier-a-clean; pip-audit ... (23 known vulnerabilities, ledgered); pytest tests/ -v (395 passed, 3 skipped, 17 warnings). Non-zero pass; consumed fresh genai-vanilla upstream bump, fixed S2 fallback after notebook magics/shell lines, and kept live Pages/default-branch drift plus known modernization/reproducibility items deferred; zero-issue streak reset
11 genuine 3 Fresh report-only subagents reviewed active/archive notebooks, docs/published surfaces, tooling/security/dependency contracts, and Python code/tests/complexity; local trace covered branch/upstream parity, genai-vanilla pinned/upstream parity, 51 notebook JSON parse, active/archive guard state, verifier S2 cell-magic and relative-import behavior, live Pages/About/default-branch state, GitHub Actions branch signal, shell/script contracts, and standard validation. Validation: red/green S2 non-Python cell-magic and relative-import regressions; focused S2 tests (4 passed); git ls-remote confirmed genai-vanilla d8ddd8e; python scripts/verify_repo.py --check all --fast (0 errors, 4 known warnings); ruff check . --no-cache; make docs-build; shell/script syntax and lint; python -m py_compile ...; pytest tests/ -v (397 passed, 3 skipped, 17 warnings); pip-audit ... (23 known vulnerabilities, ledgered). Non-zero pass; fixed S2 false positives for non-Python cell magics, added explicit notebook-relative-import findings, documented upstream genai-vanilla stale ml-lab comments as deferred, and kept live Pages/default-branch drift plus known modernization/reproducibility items deferred; zero-issue streak reset
12 genuine 3 Fresh report-only subagents reviewed active/archive notebooks, docs/published surfaces, tooling/security/dependency contracts, and Python code/tests/complexity; local trace covered branch/upstream parity, genai-vanilla upstream drift, 51 notebook JSON parse, verifier S2 dotted-relative behavior, consumed shell entrypoint lint coverage, live Pages/About/default-branch state, GitHub Actions branch signal, and standard validation. Validation: red/green S2 dotted-relative regression; red/green E6 consumed-vendor-entrypoint target regression; git ls-remote found genai-vanilla 2bee051; pinned JupyterHub requirements/Dockerfile still contain thekaveh-nnx[lm]==0.2.0, notebook runtime deps, en_core_web_sm, and vader_lexicon; python scripts/verify_repo.py --check all --fast (0 errors, 4 known warnings); python scripts/verify_repo.py --check execution --fast (0 findings); focused S2 tests (5 passed); focused E6 test passed; ruff check . --no-cache; make docs-build; shell/script syntax and lint; python -m py_compile ...; git diff --check; make check-tier-a-clean; pip-audit ... (23 known vulnerabilities, ledgered); pytest tests/ -v (399 passed, 3 skipped, 17 warnings). Non-zero pass; consumed fresh genai-vanilla upstream bump, fixed S2 dotted-relative import detection, extended E6 shellcheck coverage to consumed vendor entrypoints, and kept live Pages/default-branch drift plus known modernization/reproducibility items deferred; zero-issue streak reset
13 genuine 4 Fresh report-only subagents reviewed active/archive notebooks, docs/published surfaces, tooling/security/dependency contracts, and Python code/tests/complexity; local trace covered branch/upstream parity, genai-vanilla pinned/upstream parity, 51 notebook JSON parse, verifier S2 relative-import dedupe/fallback/line-location behavior, consumed shell dispatcher lint coverage, live Pages/About/default-branch state, GitHub Actions branch signal, and standard validation. Validation: red/green S2 one-based line, relative-dedupe, and multiline-string fallback regressions; red/green E6 dispatcher target regression; focused S2 regression group (8 passed); focused E6 test passed; git ls-remote confirmed genai-vanilla 2bee051; python scripts/verify_repo.py --check all --fast (0 errors, 4 known warnings); ruff check . --no-cache; make docs-build; shell/script syntax and lint; python -m py_compile ...; git diff --check; make check-tier-a-clean; pip-audit ... (23 known vulnerabilities, ledgered); pytest tests/ -v (402 passed, 3 skipped, 17 warnings). Non-zero pass; fixed S2 relative-import dedupe, S2 fallback multiline-string false positives, S2 one-based line locations, and E6 shellcheck coverage for the vendor dispatcher; zero-issue streak reset
14 genuine 3 Fresh report-only subagents reviewed notebooks/examples, docs/published surfaces, tooling/security/dependency contracts, and verifier/tests. Local trace covered branch/upstream parity, genai-vanilla upstream drift from 2bee051 to a22b182, the upstream delta (Capture Browserless deferred decision (#298)), JupyterHub runtime contract files including the image startup.sh entrypoint, quantization notebook run instructions, live Pages/default-branch state, GitHub Actions branch signal, and standard validation. Validation: red/green E6 vendor-image-entrypoint target regression; python scripts/verify_repo.py --check all --fast (0 errors, 4 known warnings); ruff check . --no-cache; make docs-build; expanded shellcheck/syntax pass including vendor startup.sh; python -m py_compile ...; git diff --check; make check-tier-a-clean; pip-audit ... (23 known vulnerabilities, ledgered); pytest tests/ -v (402 passed, 3 skipped, 17 warnings); gh run list still shows the stale CI failure at 2df1c9b...; live Pages still returns 404. Non-zero pass; consumed fresh genai-vanilla upstream bump, added E6 shellcheck coverage for the consumed JupyterHub image entrypoint, and fixed quantization README run instructions; zero-issue streak reset
15 genuine 3 Fresh report-only subagents reviewed active/archive notebooks, docs/published surfaces, tooling/security/dependency contracts, and Python verifier/tests. Local trace covered branch/upstream parity, genai-vanilla pinned/upstream parity at a22b182, 51 notebook parse/surface checks, live Pages/default-branch state, GitHub Actions branch signal, E6 missing-submodule behavior, S3 repo-escaping links, and S2 runtime-only import noise. Validation: red/green S3 repo-escape regression; red/green E6 missing required vendor-target regression; red/green S2 acknowledged runtime-only import regression; focused verifier regressions (4 passed); python scripts/verify_repo.py --check all --fast (0 findings); ruff check . --no-cache; make docs-build; expanded shellcheck/syntax pass including vendor startup.sh; .github/workflows/ci.yml YAML parse; python -m py_compile ...; git diff --check; make check-tier-a-clean; pip-audit ... (23 known vulnerabilities, ledgered); pytest tests/ -v (405 passed, 3 skipped, 17 warnings); live Pages still returns 404; stale branch CI signal remains from 2df1c9b.... Non-zero pass; fixed CI/submodule verifier coverage, changelog repo-escape link hygiene, and recurring torch_sparse runtime-only warning noise; zero-issue streak reset
16 genuine 8 Fresh report-only subagents reviewed active/archive notebooks, docs/published surfaces, tooling/security/dependency contracts, and Python code/tests/complexity; local trace covered branch/upstream parity, genai-vanilla upstream drift from a22b182 to 448333d, the upstream delta (Capture Supabase Edge Functions deferred decision (#299)), JupyterHub runtime contract files, stale current-runtime pin references, 51 notebook JSON parse, active/archive notebook relative guidance, live Pages/About/default-branch state, GitHub Actions branch signal, CI test surface, pip-audit automation state, root pytest collection behavior, and standard validation. Validation: python scripts/verify_repo.py --check all --fast (0 findings); python scripts/verify_repo.py --check structure --fast (0 findings); root python -m pytest --collect-only -q -p no:cacheprovider (408 tests collected); focused affected tests (17 passed); ruff check . --no-cache; make docs-build; shellcheck/syntax pass including vendor startup.sh; python -m py_compile ...; workflow/override YAML parse; notebook JSON parse (51, 0 errors); git diff --check; staged make check-tier-a-clean; pip-audit ... (23 known vulnerabilities, ledgered); pytest tests/ -v (405 passed, 3 skipped, 17 warnings); JupyterHub runtime content at 448333d re-verified (thekaveh-nnx[lm]==0.2.0, notebook runtime deps, en_core_web_sm, vader_lexicon); current runtime docs updated to the new pin. Non-zero pass; consumed fresh genai-vanilla upstream bump, updated current runtime docs/contract ledger, fixed archive/active notebook guidance, tightened root pytest behavior and helper import hygiene, documented CI/full-test and nnx public-import modernization gaps as deferred; zero-issue streak reset
17 genuine 5 Fresh report-only subagents reviewed notebooks/runtime docs, repo docs/published surfaces, tooling/CI/dependency contracts, and Python verifier/tests; local trace covered branch/upstream parity, genai-vanilla pinned/upstream parity at 448333d, active per-task runtime docs, vendor-finding docs, E6 shellcheck missing-binary behavior, docs-only CI dependency resolution, live Pages/default-branch README state, root pytest collection, shell/YAML/notebook parse, and audit surfaces. Validation: focused E6 regressions (3 passed); python scripts/verify_repo.py --check all --fast (0 findings); root python -m pytest --collect-only -q -p no:cacheprovider (409 tests collected); ruff check . --no-cache; make docs-build; shellcheck/syntax pass over local and consumed vendor scripts; python -m py_compile ...; workflow/override YAML parse; notebook JSON parse (51); git diff --check; make check-tier-a-clean; pip-audit -r docs-requirements.txt (0 known vulnerabilities); pip-audit -r requirements.txt -r torch-requirements.txt (23 known vulnerabilities, ledgered); pytest tests/ -v (406 passed, 3 skipped, 17 warnings). Non-zero pass; fixed a stale per-task runtime pin, clarified OM-053 current-pin wording, surfaced deferred vendor findings, made missing required shell targets independent of local shellcheck, and split docs CI onto a docs-only dependency surface; zero-issue streak reset
18 genuine 6 Fresh report-only subagents reviewed notebook/archive execution flow, docs/published surfaces, tooling/CI/dependency contracts, and Python verifier/rewrite tests; local trace covered branch/upstream parity, genai-vanilla upstream drift from 448333d to 0bc3abd, the upstream delta (Capture OpenLIT deferred decision (#300)), JupyterHub runtime contract files, archive CodeXGLUE path anchoring and rerun gates, verifier --repo-root config behavior, rewrite-import parenthesized inline-comment behavior, root pytest collection, shell/YAML/notebook parse, and audit surfaces. Validation: red/green pass-18 regressions; affected verifier/rewrite suite (86 passed); archive guard group (5 passed, 3 warnings); python scripts/verify_repo.py --check all --fast (0 findings); root python -m pytest --collect-only -q -p no:cacheprovider (413 tests collected); ruff check . --no-cache; make docs-build; shellcheck/syntax pass over local and consumed vendor scripts; python -m py_compile ...; workflow/config/override YAML parse; notebook JSON parse (51); git diff --check; make check-tier-a-clean; pip-audit -r docs-requirements.txt (0 known vulnerabilities); pip-audit -r requirements.txt -r torch-requirements.txt (23 known vulnerabilities, ledgered); pytest tests/ -v (410 passed, 3 skipped, 17 warnings). Non-zero pass; consumed fresh genai-vanilla upstream bump, updated current runtime docs and the maintenance log, made archived CodeXGLUE notebooks CWD-resilient and read-only by default, fixed alternate-repo verifier config loading, and made import rewriting handle inline comments; zero-issue streak reset
19 genuine 6 Fresh report-only subagents reviewed active/archive notebooks, docs/published surfaces, tooling/CI/dependency contracts, and Python verifier/rewrite complexity; local trace covered branch/upstream parity, genai-vanilla upstream drift from 0bc3abd to 2997143, JupyterHub runtime contract files, active notebook kernel metadata, stale repo-name/doc links, rewrite-import edge cases, S2 dynamic literal import coverage, root pytest collection, shell/YAML/notebook parse, and audit surfaces. Validation: focused pass-19 regressions (3 passed); affected verifier/rewrite suite (89 passed); python scripts/verify_repo.py --check all --fast (0 findings); root python -m pytest --collect-only -q -p no:cacheprovider (416 tests collected); ruff check . --no-cache; make docs-build; shellcheck/syntax pass over local and consumed vendor scripts; python -m py_compile ...; workflow/config/override YAML parse; notebook JSON parse (51); active notebook metadata scan (29, 0 mismatches); git diff --check; staged make check-tier-a-clean; pip-audit -r docs-requirements.txt (0 known vulnerabilities); pip-audit -r requirements.txt -r torch-requirements.txt (23 known vulnerabilities, ledgered); pytest tests/ -v (413 passed, 3 skipped, 17 warnings). Non-zero pass; consumed fresh genai-vanilla upstream bump, normalized active notebook runtime metadata, refreshed current runtime docs and repo-name links, fixed two rewrite-import blind spots, and added S2 literal dynamic-import coverage; zero-issue streak reset
20 genuine 3 Fresh report-only subagents reviewed notebooks/runtime behavior, docs/published surfaces, tooling/CI/supply-chain, and Python verifier/rewrite complexity; local trace covered branch/upstream parity, current genai-vanilla pin, active/archive notebook metadata and rerun guards, stale-token sweeps, single-line parenthesized import rewrites, dynamic literal import aliases, ignored docs/superpowers/plans link hygiene, root pytest collection, shell/YAML/notebook parse, and audit surfaces. Validation: red/green pass-20 regressions (3 failed before fixes, then passed); affected verifier/rewrite suite (92 passed); ignored plan-doc link checker (53 broken before, 0 after local cleanup); python scripts/verify_repo.py --check all --fast (0 findings); root python -m pytest --collect-only -q -p no:cacheprovider (419 tests collected); ruff check . --no-cache; make docs-build; shellcheck/syntax pass over local and consumed vendor scripts; python -m py_compile ...; workflow/config/override YAML parse; notebook JSON parse (51); git diff --check; make check-tier-a-clean; pip-audit -r docs-requirements.txt (0 known vulnerabilities); pip-audit -r requirements.txt -r torch-requirements.txt (23 known vulnerabilities, ledgered); pytest tests/ -v (416 passed, 3 skipped, 17 warnings). Non-zero pass; fixed single-line parenthesized import rewriting, extended S2 dynamic-import coverage to common importlib aliases, and cleaned ignored superpowers-plan local links; zero-issue streak reset
21 genuine 4 Fresh report-only subagents reviewed notebook/runtime docs, docs/published surfaces, tooling/submodule contracts, and Python verifier/rewrite behavior; local trace covered branch/upstream parity, genai-vanilla upstream drift from 2997143 to 1631344, the upstream delta (Capture FinRL FinGPT notebook deferral (#302)), JupyterHub runtime contract files, dirty submodule verifier coverage, S2 SyntaxError fallback alias behavior, notebook source-list chunk rewriting, root pytest collection, shell/YAML/notebook parse, and audit surfaces. Validation: red/green pass-21 regressions (3 failed before fixes, then passed); affected verifier/rewrite suite (95 passed); python scripts/verify_repo.py --check all --fast (0 findings); git submodule status vendor/genai-vanilla showed clean 1631344; root python -m pytest --collect-only -q -p no:cacheprovider (422 tests collected); ruff check . --no-cache; make docs-build; shellcheck/syntax pass over local and consumed vendor scripts; python -m py_compile ...; workflow/config/override YAML parse; notebook JSON parse (51); git diff --cached --check && git diff --check; make check-tier-a-clean; pip-audit -r docs-requirements.txt (0 known vulnerabilities); pip-audit -r requirements.txt -r torch-requirements.txt (23 known vulnerabilities, ledgered); pytest tests/ -v (419 passed, 3 skipped, 17 warnings). Non-zero pass; consumed fresh genai-vanilla upstream bump, updated current runtime docs and dependency ledger, made E6 flag dirty required submodules, fixed S2 fallback alias dynamic imports, and preserved notebook list-source chunks during import rewriting; zero-issue streak reset
22 genuine 4 Fresh report-only subagents reviewed notebooks/runtime contracts, docs/published surfaces, tooling/supply-chain, and Python verifier/rewrite behavior; local trace covered branch/upstream parity, genai-vanilla pinned/upstream parity at 1631344, notebook JSON and root collection, stale repo-name/runtime-pin sweeps, live Pages/About/CI state, S2 fallback parsing, rewrite-import source chunking, submodule dirty-state coverage, and audit surfaces. Validation: red/green pass-22 regressions (3 failed before fixes, then passed); affected verifier/rewrite suite (98 passed); python scripts/verify_repo.py --check all --fast (0 findings); root python -m pytest --collect-only -q -p no:cacheprovider (425 tests collected); ruff check . --no-cache; make docs-build; shellcheck/syntax pass over local and consumed vendor scripts; python -m py_compile ...; workflow/config/override YAML parse; notebook JSON parse (51); git diff --check; make check-tier-a-clean; pip-audit -r docs-requirements.txt (0 known vulnerabilities); pip-audit -r requirements.txt -r torch-requirements.txt (23 known vulnerabilities, ledgered); pytest tests/ -v (422 passed, 3 skipped, 17 warnings). Non-zero pass; fixed stale OM-053 current-pin wording, made S2 fallback track multiline importlib aliases, joined notebook source chunks before import rewriting, and made E6 flag local modifications inside required submodules; zero-issue streak reset
23 genuine 4 Fresh report-only subagents reviewed notebooks/runtime contracts, docs/published surfaces, tooling/supply-chain, and Python verifier behavior; local trace covered branch/upstream parity, genai-vanilla upstream drift from 1631344 to b96a292, runtime-file delta checks, JupyterHub requirement/Dockerfile contracts, S2 fallback parsing, dependency-ledger SHA/gitlink consistency, submodule worktree test coverage, root collection, shell/YAML/notebook parse, and audit surfaces. Validation: red/green pass-23 regressions (2 failed, 1 passed coverage guard before fixes, then 3 passed); affected verifier/rewrite suite (100 passed); python scripts/verify_repo.py --check all --fast (0 findings after staging the gitlink); root python -m pytest --collect-only -q -p no:cacheprovider (427 tests collected); ruff check . --no-cache; make docs-build; shellcheck/syntax pass over local and consumed vendor scripts; python -m py_compile ...; workflow/config/override YAML parse; notebook JSON parse (51); git diff --cached --check && git diff --check; make check-tier-a-clean; pip-audit -r docs-requirements.txt (0 known vulnerabilities); pip-audit -r requirements.txt -r torch-requirements.txt (23 known vulnerabilities, ledgered); pytest tests/ -v (424 passed, 3 skipped, 17 warnings). Non-zero pass; consumed fresh genai-vanilla upstream bump, updated current runtime docs/dependency ledger, added D10 ledger-vs-gitlink verification, fixed S2 fallback multiline dynamic import calls, and tightened the submodule worktree test's cwd assertion; zero-issue streak reset
24 genuine 3 Fresh report-only subagents reviewed notebook/runtime contracts, docs/published surfaces, tooling/supply-chain, and Python verifier behavior; local trace covered branch/upstream parity, genai-vanilla upstream drift from b96a292 to ba21661, runtime-file delta checks, JupyterHub requirement/Dockerfile contracts, D10 malformed-ledger behavior, S2 SyntaxError fallback continuation behavior, root collection, shell/YAML/notebook parse, and audit surfaces. Validation: red/green pass-24 regressions (2 failed before fixes, then 5 passed across focused D10/S2 guards); affected verifier/rewrite suite (102 passed); python scripts/verify_repo.py --check all --fast (0 findings after staging the gitlink); root python -m pytest --collect-only -q -p no:cacheprovider (429 tests collected); ruff check . --no-cache; make docs-build; shellcheck/syntax pass over local and consumed vendor scripts; python -m py_compile ...; workflow/config/override YAML parse; notebook JSON parse (51); git diff --cached --check && git diff --check; make check-tier-a-clean; pip-audit -r docs-requirements.txt (0 known vulnerabilities); pip-audit -r requirements.txt -r torch-requirements.txt (23 known vulnerabilities, ledgered); pytest tests/ -v (426 passed, 3 skipped, 17 warnings). Non-zero pass; consumed fresh genai-vanilla upstream bump, updated current runtime docs/dependency ledger, made D10 fail closed when the ledger omits a parseable genai-vanilla SHA, and fixed S2 fallback backslash-continued multi-import parsing; zero-issue streak reset
25 genuine 3 Fresh report-only subagents reviewed notebook/runtime contracts, docs/published surfaces, tooling/supply-chain, and Python verifier/rewrite behavior; local trace covered branch/upstream parity, genai-vanilla latest-vs-pinned drift from ba21661 to 329f883, intentional stale ml-lab vendor-comment findings, PASSES=20 header semantics, rewrite-import explicit continuation behavior, D10 gitlink parse behavior, root collection, shell/YAML/notebook parse, and audit surfaces. Validation: red/green pass-25 regressions (2 failed before fixes, then 2 passed); affected verifier/rewrite suite (104 passed); python scripts/verify_repo.py --check all --fast (0 findings); root python -m pytest --collect-only -q -p no:cacheprovider (431 tests collected); ruff check . --no-cache; make docs-build; shellcheck/syntax pass over local and consumed vendor scripts; python -m py_compile ...; workflow/config/override YAML parse; notebook JSON parse (51); git diff --cached --check && git diff --check; make check-tier-a-clean; pip-audit -r docs-requirements.txt (0 known vulnerabilities); pip-audit -r requirements.txt -r torch-requirements.txt (23 known vulnerabilities, ledgered); pytest tests/ -v (428 passed, 3 skipped, 17 warnings). Non-zero pass; fixed rewrite-import call-site rewriting for explicit backslash continuations, made D10 fail closed when the genai-vanilla gitlink cannot be parsed, and consumed the fresh genai-vanilla Honcho research-doc bump; zero-issue streak reset
26 genuine 0 Fresh report-only subagents reviewed notebook/runtime contracts, docs/published surfaces, tooling/supply-chain, and Python verifier/rewrite behavior; local trace covered branch/upstream parity, genai-vanilla latest-vs-pinned parity at 329f883, intentional stale ml-lab vendor-comment findings, active/archive notebook path and rerun guards, MkDocs nav and local links, workflow action pins, audit ledger counts, shell entrypoints, rewrite-import and verifier regression coverage, and complexity hotspots. Validation: python scripts/verify_repo.py --check all --fast (0 findings); pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q (104 passed); subagent pytest -q (428 passed, 3 skipped); docs reviewer link/nav/numbering checks (79 internal links, 0 broken; 13 nav entries, 0 missing); notebook reviewer parsed 51 notebooks and scanned all 29 active notebooks for stale path/name/CWD hazards; tooling reviewer confirmed pip-audit still matches the ledgered 23 vulnerabilities; branch/upstream parity 0 0. Zero-issue pass; OM-053 vendor-comment limitation remains documented/deferred and was not counted as new; zero-issue streak 1/20
27 genuine 0 Fresh report-only subagents reviewed notebook/runtime contracts, docs/published surfaces, tooling/supply-chain, and Python verifier/rewrite behavior; local trace covered branch/upstream parity, genai-vanilla latest-vs-pinned parity at 329f883, intentional stale ml-lab vendor-comment findings, active notebook relative-path scans, archive rerun guards, MkDocs/nav/link/numbering checks, workflow action pins, audit ledger counts, shell entrypoints, verifier fallback parsing, D10 ledger checks, and rewrite-import continuation coverage. Validation: python scripts/verify_repo.py --check all --fast (0 findings); pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q (104 passed); docs reviewer mkdocs build --strict and link/nav checks (79 internal links, 0 broken; 13 nav entries, 0 missing); notebook reviewer scanned 29 active notebooks and sampled archive guards; tooling reviewer confirmed pip-audit still matches the ledgered 23 vulnerabilities and workflow action pins match documented tags; Python reviewer confirmed ruff and helper probes; branch/upstream parity 0 0. Zero-issue pass; OM-053 remains documented/deferred and was not counted as new; zero-issue streak 2/20
28 genuine 2 Fresh report-only subagents reviewed notebook/runtime behavior, docs/published surfaces, tooling/supply-chain, and Python verifier/rewrite behavior; local trace covered branch/upstream parity, genai-vanilla latest-vs-pinned parity at 329f883, active/archive notebook scans, validation-log ordering, workflow pins, audit ledger counts, shell/YAML checks, and rewrite-import cell-magic behavior. Validation: red/green rewrite regression failed before the fix and passed after; affected verifier/rewrite suite passed (105 passed); pass-28 docs issue corrected the validation log chronology. Non-zero pass; fixed pass-18 validation-log ordering and preserved first-line Jupyter cell magics during NNParams import injection; zero-issue streak reset to 0/20; complexity comments remain covered by existing OM-022 deferred debt
29 genuine 3 Fresh report-only subagents reviewed notebooks/runtime contracts, docs/published surfaces, tooling/supply-chain, and Python verifier/rewrite behavior; local trace covered branch/upstream parity, genai-vanilla upstream drift from 329f883 to c2ffe8d, JupyterHub runtime-file contracts, README clean-checkout wording for task-local data/ and runs/, rewrite-import parenthesized mixed closing-line behavior, workflow pins, audit ledger counts, shell entrypoints, and affected tests. Validation: red/green pass-29 regressions failed before fixes and passed after; affected verifier/rewrite suite passed (107 passed). Non-zero pass; consumed the Redis Stack/RedisInsight genai-vanilla research-doc bump, fixed README runtime-artifact wording, and preserved kept symbols on mixed parenthesized import closing lines; zero-issue streak remains 0/20
30 genuine 2 Fresh report-only subagents reviewed notebooks/runtime contracts, docs/published surfaces, tooling/supply-chain, and Python verifier/rewrite behavior; local trace covered branch/upstream parity, genai-vanilla upstream drift from c2ffe8d to 10f8402, JupyterHub runtime-file contracts, maintenance-log/documentation consistency, workflow pins, audit ledger counts, shell entrypoints, and existing parenthesized NNParams import behavior. Validation: red/green pass-30 rewrite regression failed before the fix and passed after; affected verifier/rewrite suite passed (108 passed). Non-zero pass; consumed the Perplexica/Vane genai-vanilla research-doc bump and prevented duplicate NNParams imports when an existing parenthesized import closes on the same line; zero-issue streak remains 0/20
31 genuine 1 Fresh report-only subagents reviewed notebooks/runtime contracts, docs/published surfaces, tooling/supply-chain, and Python verifier/rewrite behavior; local trace covered branch/upstream parity, genai-vanilla latest-vs-pinned parity at 10f8402, README/runtime-doc pin consistency, notebook path/rerun contracts, workflow pins, audit ledger counts, shell entrypoints, and parenthesized import opener-line behavior. Validation: red/green pass-31 rewrite regression failed before the fix and passed after; affected verifier/rewrite suite passed (109 passed). Non-zero pass; rewrote deprecated Params members that appear on parenthesized import opener lines; zero-issue streak remains 0/20
32 genuine 6 Fresh report-only subagents reviewed notebooks/runtime artifact behavior, docs/published surfaces, tooling/supply-chain contracts, and Python verifier/rewrite behavior; local trace covered branch/upstream parity, genai-vanilla latest-vs-pinned parity at 10f8402, notebook metadata/path/rerun contracts, README runtime-artifact policy, workflow action pins, S2 dotted-import behavior, and rewrite-import call/import edge cases. Validation: red/green pass-32 regressions failed before fixes and passed after; affected verifier/rewrite suite passed (116 passed); full pytest passed (440 passed, 3 skipped, 17 warnings). Non-zero pass; documented task-local smoke artifacts, tightened rewrite call/import preservation, checked dotted submodule imports, made missing rewrite inputs fail, and added workflow action-pin enforcement; zero-issue streak remains 0/20
33 genuine 2 Fresh report-only subagents reviewed notebook/runtime contracts, docs/published surfaces, tooling/supply-chain contracts, and Python verifier/rewrite behavior after pass 32; local trace covered branch/upstream parity, genai-vanilla latest-vs-pinned parity at 10f8402, maintenance-log chronology, action-pin enforcement, workflow extension coverage, and deprecated Params non-call references. Validation: red/green pass-33 regressions failed before fixes and passed after; affected verifier/rewrite suite passed (118 passed); full pytest passed (442 passed, 3 skipped, 17 warnings). Non-zero pass; extended action-pin enforcement to .yaml workflows and rewrote unqualified deprecated Params references after import migration; zero-issue streak remains 0/20
34 genuine 1 Fresh report-only subagents reviewed notebook/runtime contracts, docs/published surfaces, tooling/build/supply-chain contracts, and Python verifier/rewrite behavior; local trace covered branch/upstream parity, genai-vanilla latest-vs-pinned parity at 10f8402, 51 notebook JSON parse, maintenance-log chronology, docs links and repo-name migration, workflow pins, shell/YAML checks, compose-config validation, audit ledger counts, and full tests. Validation: python scripts/verify_repo.py --check all --fast (0 findings); pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q (118 passed); pytest tests/ -v (442 passed, 3 skipped, 17 warnings); ruff check . --no-cache; make docs-build; python -m compileall scripts tests notebooks -q; git diff --check; notebook JSON parse (51); YAML parse; shellcheck/syntax pass; pip-audit -r docs-requirements.txt (0 known vulnerabilities); runtime audit still matched the ledgered 23 known vulnerabilities. Non-zero pass; fixed the genai-vanilla compose-config upgrade checklist so it includes the required env file; zero-issue streak remains 0/20
35 genuine 2 Fresh report-only subagents reviewed notebook/runtime contracts, docs/published surfaces, tooling/build/supply-chain contracts, and Python verifier/rewrite behavior; local trace covered branch/upstream parity, genai-vanilla latest-vs-pinned parity at 10f8402, 51 notebook JSON parse, maintenance-log chronology, docs links and repo-name migration, workflow pins, shell/YAML checks, compose-config validation, audit ledger counts, and rewrite-import preservation behavior. Validation: red/green pass-35 rewrite regressions failed before fixes and passed after; pytest tests/test_rewrite_imports.py -q passed (31 passed); affected verifier/rewrite suite passed (120 passed); python scripts/verify_repo.py --check all --fast reported 0 findings; post-fix full pytest passed (444 passed, 3 skipped, 17 warnings). Non-zero pass; preserved no-op single-line parenthesized imports and kept comments in changed parenthesized import blocks; zero-issue streak remains 0/20
36 genuine 1 Fresh report-only subagents reviewed notebook/runtime contracts, docs/published surfaces, tooling/build/supply-chain contracts, and Python verifier/rewrite behavior; local trace covered branch/upstream parity, genai-vanilla latest-vs-pinned parity at 10f8402, 51 notebook JSON parse, maintenance-log chronology, workflow pins, shell/YAML checks, compose-config validation, audit ledger counts, and S5/rewrite import alias coverage. Validation: pass-36 regressions for comma-separated common imports failed before fixes and passed after; affected verifier/rewrite suite passed (123 passed); python scripts/verify_repo.py --check all --fast reported 0 findings. Non-zero pass; S5 now inspects every AST import alias and rewrite_imports.py migrates common aliases inside comma-separated imports; zero-issue streak remains 0/20
37 genuine 5 Fresh report-only subagents reviewed notebook/runtime contracts, docs/published surfaces, tooling/build/supply-chain contracts, and Python verifier/rewrite behavior; local trace covered branch/upstream parity, genai-vanilla latest-vs-pinned parity at 10f8402, issue-count reconciliation, rewrite idempotence around non-Python text, S2 fallback parsing, notebook JSON parse, shell/YAML checks, compose-config validation, and audit ledger counts. Validation: pass-37 regressions for multiline strings, non-Python cell magics, aliased NNParams imports, fallback comment parentheses, and closing-paren comments failed before fixes and passed after; python scripts/verify_repo.py --check all --fast reported 0 findings. Non-zero pass; hardened rewrite/verifier edge cases and corrected historical pass-history issue accounting; zero-issue streak remains 0/20
38 genuine 4 Fresh report-only subagents reviewed notebook/runtime contracts, docs/published surfaces, tooling/build/supply-chain contracts, and Python verifier/rewrite behavior; local trace covered branch/upstream parity, genai-vanilla latest-vs-pinned parity at 10f8402, S1 notebook schema validation, Reddit notebook metadata, rewrite binding-position behavior, from common import utils migration, notebook JSON/schema validation, shell/YAML checks, compose-config validation, and audit ledger counts. Validation: pass-38 regressions for local binding preservation, from common import utils, and invalid notebook schema failed before fixes and passed after; python scripts/verify_repo.py --check all --fast reported 0 findings. Non-zero pass; repaired Reddit notebook schema metadata, added S1 schema validation, and tightened rewrite-import edge cases; zero-issue streak remains 0/20
39 genuine 2 Fresh report-only subagents reviewed notebook/runtime contracts, docs/published surfaces, tooling/build/supply-chain contracts, and Python verifier/rewrite behavior; local trace covered branch/upstream parity, S1 archive schema scope, deprecated Params import rewriting with local bindings, notebook schema validation, and affected verifier/rewrite coverage. Validation: pass-39 regressions for mixed imported/local deprecated Params names and archive missing cell IDs failed before fixes and passed after; affected verifier/rewrite suite passed (133 passed); python scripts/verify_repo.py --check structure --fast reported 0 findings; all 51 notebooks schema-validated with cell IDs. Non-zero pass; promoted archived notebook cell IDs to raw nbformat fields, expanded S1 schema checks across notebooks/**/*.ipynb, and made deprecated Params rewrite protection position-aware; zero-issue streak remains 0/20
40 genuine 3 Fresh report-only subagents reviewed notebook/runtime contracts, docs/published surfaces, tooling/build/supply-chain contracts, and Python verifier/rewrite behavior; local trace covered branch/upstream parity, published-doc heading coverage, architecture nav numbering, rewrite continuation binding protection, notebook schema validation, shell/YAML/compose checks, audit ledger counts, and full tests. Validation: pass-40 regressions for continued local bindings after import-drop rewrites and malformed published-doc H2 numbering failed before fixes and passed after; affected verifier/rewrite suite passed (135 passed); python scripts/verify_repo.py --check all --fast reported 0 findings. Non-zero pass; recomputed continuation binding protection after line-dropping rewrites, extended D9 to published MkDocs pages, normalized overview/architecture headings, and kept zero-issue streak at 0/20
41 genuine 2 Fresh report-only subagents reviewed notebook/runtime contracts, docs/published surfaces, tooling/build/supply-chain contracts, and Python verifier/rewrite behavior; local trace covered branch/upstream parity, function/class shadowing in rewrite binding protection, published diagram provenance D9 coverage, notebook schema validation, shell/YAML/compose checks, audit ledger counts, and full tests. Validation: pass-41 regressions for local class/function bindings after import-drop rewrites and malformed diagram provenance H2 numbering failed before fixes and passed after; affected verifier/rewrite suite passed (137 passed); python scripts/verify_repo.py --check all --fast reported 0 findings. Non-zero pass; protected local function/class definitions during deprecated Params rewrites, added diagram provenance to D9 coverage, and kept zero-issue streak at 0/20
42 genuine 3 Fresh report-only subagents reviewed notebook/runtime contracts, docs/published surfaces, tooling/build/supply-chain contracts, and Python verifier/rewrite behavior; local trace covered branch/upstream parity, Python function-scope local binding semantics, cross-language archive output/artifact parity, Makefile interpreter override behavior, notebook schema validation, shell/YAML/compose checks, audit ledger counts, and full tests. Validation: pass-42 regressions for function-local deprecated Params reads before assignment, stale archive outputs with missing model artifacts, and setup-target PYTHON overrides failed before fixes and passed after; affected suites passed (341 passed); python scripts/verify_repo.py --check all --fast reported 0 findings; full pytest passed (464 passed, 3 skipped, 17 warnings). Non-zero pass; protected whole function/lambda/comprehension scopes during deprecated Params rewrites, refreshed missing-artifact archive outputs, routed setup targets through the selected Python interpreter, and kept zero-issue streak at 0/20
43 genuine 0 Local pass reviewed branch/upstream parity, verifier output, rewrite/notebook/Makefile regression coverage, full pytest, ruff, strict docs build, compileall, notebook JSON parse, stale repo-name sweep, whitespace checks, and maintenance-log continuity after the pass-42 reset. Validation: git status --short --branch was clean; git rev-list --left-right --count @{u}...HEAD returned 0 0; python scripts/verify_repo.py --check all --fast reported 0 findings; focused pass-42 regression suites passed (341 passed, 3 warnings); full pytest -q passed (464 passed, 3 skipped, 17 warnings); ruff check . --no-cache, make docs-build, python -m compileall scripts tests notebooks -q, git diff --check, and notebook JSON parse (51) passed. Zero-issue pass; OM-053 vendor-comment limitation remains documented/deferred and was not counted as new; zero-issue streak 1/20
44 genuine 0 Local pass reviewed branch/upstream parity, genai-vanilla upstream/submodule parity, repo verifier output, Markdown local links, published-doc numbered headings, notebook source path hazards, workflow/config YAML parsing, rewrite/verifier/notebook/Makefile regression coverage, shell entrypoints, compose config, audits, and full tests. Validation: branch/upstream returned 0 0; genai-vanilla local and upstream both resolved to 10f8402; python scripts/verify_repo.py --check all --fast reported 0 findings; focused regression suite passed (437 passed, 3 warnings); full pytest -q passed (464 passed, 3 skipped, 17 warnings); ruff check . --no-cache, make docs-build, compileall, notebook JSON parse (51), YAML parse, shellcheck/syntax, compose config, and docs audit passed. Zero-issue pass; runtime pip-audit still matches the ledgered 23 accepted findings; zero-issue streak 2/20
45 genuine 0 Local pass revisited the notebook reorganization and repo rename goals: project notebook placement, archive placement, task-local data/runs structure, tracked artifact hygiene, relative artifact references, stale ml-lab references outside documented/deferred surfaces, verifier output, full tests, docs, compile, notebook JSON, YAML, compose config, and whitespace checks. Validation: branch/upstream returned 0 0; project notebooks outside notebooks/ count was 0; task-local data/runs structural issues were 0; tracked notebooks/**/{data,runs,__pycache__} artifacts were absent; relative artifact/CWD hazard scan found 0 hits; stale-name sweep found only the verifier detector pattern outside excluded historical/vendor docs; python scripts/verify_repo.py --check all --fast reported 0 findings; full pytest -q passed (464 passed, 3 skipped, 17 warnings). Zero-issue pass; notebook organization and relative-artifact contracts remain clean; zero-issue streak 3/20
46 genuine 0 Local pass reviewed tooling and CI contracts: branch/upstream parity, verifier output, root pytest collection boundaries, Tier-A cleanliness target, Makefile dry-run behavior, ruff, strict docs build, compileall, shell entrypoints, docs dependency audit, whitespace, and full tests. Validation: branch/upstream returned 0 0; python scripts/verify_repo.py --check all --fast reported 0 findings; root python -m pytest --collect-only -q -p no:cacheprovider collected 467 intended tests without vendored collection; make -n check-tier-a-clean and make check-tier-a-clean targeted the configured Tier-A notebooks; ruff check . --no-cache, make docs-build, compileall, shellcheck/syntax, pip-audit -r docs-requirements.txt, git diff --check, and full pytest -q passed. Zero-issue pass; tooling/CI contracts remain clean; zero-issue streak 4/20
47 genuine 0 Local pass reviewed documentation and published surfaces: branch/upstream parity, docs verifier, full verifier, MkDocs navigation, Markdown local links, published numbered headings, current genai-vanilla/runtime wording, historical pin mentions, strict docs build, ruff, compileall, whitespace, and full tests. Validation: branch/upstream returned 0 0; python scripts/verify_repo.py --check docs --fast and --check all --fast reported 0 findings; MkDocs nav had 13 targets and 0 missing; Markdown local-link scan covered 28 files with 0 missing links; published H2 numbering issues were 0; current pin/package text was present; old SHA hits were limited to dependency-ledger history; make docs-build, ruff, compileall, git diff --check, and full pytest -q passed. Zero-issue pass; docs and published-surface contracts remain clean; zero-issue streak 5/20
48 genuine 0 Local pass reviewed Python tooling and migration helpers: branch/upstream parity, structure/full verifier output, rewrite-import regression coverage, verifier/edit/smoke/Makefile helper tests, script compilation, migration-residue scan boundaries, AST parsing for scripts/tests, ruff, strict docs build, compileall, whitespace, and full tests. Validation: branch/upstream returned 0 0; python scripts/verify_repo.py --check structure --fast and --check all --fast reported 0 findings; focused tooling suite passed (148 passed); helper scripts compiled; direct residue scan found deprecated/common migration text only in tests and the migration script itself; scripts/tests AST parsed; ruff check scripts tests --no-cache, make docs-build, compileall, git diff --check, and full pytest -q passed. Zero-issue pass; Python tooling and migration-helper contracts remain clean; zero-issue streak 6/20
49 genuine 0 Local pass reviewed notebook/runtime contracts: branch/upstream parity, execution/full verifier output, active/archive notebook API surface tests, Reddit and quantization notebook guards, nbformat schema validation, committed error outputs, transient path leaks, archive task shape, ruff, docs build, compileall, compose config, whitespace, and full tests. Validation: branch/upstream returned 0 0; python scripts/verify_repo.py --check execution --fast and --check all --fast reported 0 findings; focused notebook/runtime suite passed (302 passed, 3 skipped, 3 warnings); all 51 notebooks validated with nbformat.validate; direct scans found 0 committed error outputs and 0 transient path leaks; notebooks/archive/codexglue_summarization/src was the only archive child without a notebook and is the shared helper snapshot; ruff, make docs-build, compileall, compose config, git diff --check, and full pytest -q passed. Zero-issue pass; notebook/runtime contracts remain clean; zero-issue streak 7/20
50 genuine 0 Final hard-cap pass reviewed branch/upstream parity, genai-vanilla upstream/submodule parity, full verifier output, nbformat schema validation, ruff, strict docs build, compileall, whitespace, shell entrypoints, docs and runtime audits, compose config, and full tests. Validation: branch/upstream returned 0 0; genai-vanilla local and upstream both resolved to 10f8402; python scripts/verify_repo.py --check all --fast reported 0 findings; all 51 notebooks validated with nbformat.validate; ruff check . --no-cache, make docs-build, python -m compileall scripts tests notebooks -q, git diff --check, shellcheck/syntax, pip-audit -r docs-requirements.txt, compose config, and full pytest -q passed; runtime pip-audit still reported the ledgered 23 accepted findings. Zero-issue pass; zero-issue streak 8/20; hard cap MAX_PASSES=50 reached before the requested 20 consecutive zero-issue passes

3. Validation Log

  • pytest tests/test_verify_repo.py::test_structure_s3_checks_nested_docs_markdown_links -q failed before the docs-iterator fix and passed after it.
  • pytest tests/test_verify_repo.py::test_run_helper_supplies_default_timeout -q failed before adding the default timeout and passed after it.
  • pytest tests/test_verify_repo.py::test_runtime_available_requires_pyg_extension_stack -q failed before expanding the PyG canary and passed after it.
  • python scripts/verify_repo.py --check docs --fast: 0 findings.
  • python scripts/verify_repo.py --check all --fast: 0 errors, 4 warnings for runtime-container-only torch_sparse imports in Reddit phase3 notebooks.
  • make docs-build: passed with the upstream Material for MkDocs 2.0 warning.
  • ruff check . --no-cache: passed.
  • pytest tests/ -v: 381 passed, 3 skipped, 17 warnings.
  • make check-tier-a-clean: passed.
  • shellcheck scripts/start-jupyterhub.sh: passed.
  • python -m py_compile scripts/verify_repo.py: passed.
  • git diff --check: passed.
  • python scripts/verify_repo.py --check all --fast: 0 errors, 4 known warnings for runtime-container-only torch_sparse imports in Reddit phase3 notebooks.
  • make docs-build: passed with the upstream Material for MkDocs 2.0 warning.
  • pytest tests/ -v: 384 passed, 3 skipped, 17 warnings.
  • make check-tier-a-clean: passed.
  • shellcheck scripts/start-jupyterhub.sh: passed.
  • pip-audit -r requirements.txt -r torch-requirements.txt: 23 known vulnerabilities in the same ledgered torch, pytorch-lightning, and nltk packages.
  • pytest tests/test_numpy_layers.py -v: failed before validating supplied LinearLayer parameter shapes, then passed after the constructor fix (3 passed).
  • python - <<'PY' ... yaml.safe_load(...): parsed .github/workflows/pages.yml and .github/workflows/ci.yml.
  • pytest tests/test_numpy_layers.py tests/test_verify_repo.py -q: 60 passed.
  • python scripts/verify_repo.py --check docs --fast: 0 findings.
  • ruff check . --no-cache: passed.
  • python -m py_compile scripts/verify_repo.py: passed.
  • git diff --check: passed.
  • pytest tests/test_verify_repo.py::test_e14_flags_tmp_papermill_output_path -q: failed before adding the E14 verifier guard, then passed after it.
  • python scripts/verify_repo.py --check execution --fast: first reported 17 E14.tmp_papermill_output_path warnings, then 0 findings after stripping top-level stale papermill metadata.
  • curl -I -L https://thekaveh.github.io/ml-eng-lab/: still returned HTTP 404, matching deferred OM-011.
  • gh repo view thekaveh/ml-eng-lab --json name,description,homepageUrl,repositoryTopics,defaultBranchRef,url: default branch main, description/topics current, homepage still README pending live Pages.
  • git ls-remote --tags for pinned GitHub Actions: reviewed tag SHAs still match .github/workflows/* and docs/dependency-contracts.md.
  • git ls-remote https://github.com/thekaveh/genai-vanilla.git refs/heads/main: upstream main is b0bce0fc4e9d2bb282fbc6c97631f3e37233e24e.
  • python scripts/verify_repo.py --check all --fast: 0 errors, 4 known warnings for runtime-container-only torch_sparse imports in Reddit phase3 notebooks.
  • ruff check . --no-cache: passed.
  • make docs-build: passed with the upstream Material for MkDocs 2.0 warning.
  • pytest tests/ -v: 385 passed, 3 skipped, 17 warnings.
  • python -m py_compile scripts/verify_repo.py: passed.
  • shellcheck scripts/start-jupyterhub.sh: passed.
  • bash -n scripts/start-jupyterhub.sh: passed.
  • pip-audit -r requirements.txt -r torch-requirements.txt: 23 known vulnerabilities in the same ledgered torch, pytorch-lightning, and nltk packages.
  • Notebook JSON parse across notebooks/**/*.ipynb: passed.
  • git diff --check: passed.
  • pytest tests/nnx_surface/test_notebook_api_surface.py::test_phase2_notebook4_ranks_local_runs_not_cross_experiment_registry -q: failed before replacing NNRun.all() in Reddit phase2 notebook 4, then passed after ranking the notebook-local runs list and clearing stale dependent outputs.
  • pytest tests/nnx_surface/test_quantization_mnist_ffnn_pytorch.py -q: 3 passed, covering quantization facade signatures plus backend-gated PTQ/QAT smoke.
  • python -m json.tool notebooks/node_classification-reddit-gnn-pyg/phase2-model-selection-notebook4.ipynb >/dev/null: passed.
  • ruff check . --no-cache: first flagged the now-unused NNRun import in Reddit phase2 notebook 4, then passed after removing it.
  • python scripts/verify_repo.py --check all --fast: 0 errors, 4 known warnings for runtime-container-only torch_sparse imports in Reddit phase3 notebooks.
  • pytest tests/ -v: 389 passed, 3 skipped, 17 warnings.
  • make docs-build: passed with the upstream Material for MkDocs 2.0 warning.
  • shellcheck scripts/start-jupyterhub.sh && bash -n scripts/start-jupyterhub.sh: passed.
  • git diff --check: passed.
  • python -m py_compile scripts/verify_repo.py: passed.
  • pip-audit -r requirements.txt -r torch-requirements.txt: 23 known vulnerabilities in the same ledgered torch, pytorch-lightning, and nltk packages.
  • Notebook JSON parse across notebooks/**/*.ipynb: parsed 51 notebooks.
  • Tracked data//runs/ scan and generated-cache scan: no tracked matches.
  • make check-tier-a-clean: passed after staging the intentional Reddit phase2 notebook artifact update.
  • git ls-remote https://github.com/thekaveh/genai-vanilla.git refs/heads/main: upstream main is now 0e4e9643ac273c6f36f815a5f4b3b187876bac74.
  • git submodule status --recursive: superproject gitlink remains pinned to c89eb5e7bc53a97c9ecea668a86a4f41debe7113.
  • git ls-remote --tags for pinned GitHub Actions: actions/checkout@v7, actions/setup-python@v6, astral-sh/ruff-action@v3, actions/upload-pages-artifact@v5, and actions/deploy-pages@v5 still match workflow pins and the dependency ledger.
  • curl -I -L https://thekaveh.github.io/ml-eng-lab/: still returned HTTP 404, matching deferred OM-011.
  • gh repo view thekaveh/ml-eng-lab --json name,description,homepageUrl,repositoryTopics,defaultBranchRef,url: default branch main, description/topics current, homepage still README pending live Pages.
  • gh run list --repo thekaveh/ml-eng-lab --branch codex/overnight-maintenance --limit 10 --json ...: no fresh run for current head, matching deferred OM-012.
  • pytest tests/test_verify_repo.py::test_e14_flags_source_notebook_papermill_metadata -q: failed before broadening E14 to all active source-notebook top-level papermill metadata, then passed after the verifier guard.
  • python scripts/verify_repo.py --check execution --fast: reported 4 E14.source_papermill_metadata warnings before stripping top-level papermill metadata from active source notebooks, then 0 findings after cleanup.
  • Focused changed tests for E14, notebook helper CLIs, and tracked-notebook discovery: 13 passed, 3 warnings.
  • pytest tests/ -v: 390 passed, 3 skipped, 17 warnings.
  • python scripts/verify_repo.py --check all --fast: 0 errors, 4 known warnings for runtime-container-only torch_sparse imports in Reddit phase3 notebooks.
  • ruff check . --no-cache: passed.
  • make docs-build: passed with the upstream Material for MkDocs 2.0 warning.
  • shellcheck scripts/start-jupyterhub.sh && bash -n scripts/start-jupyterhub.sh: passed.
  • python -m py_compile scripts/verify_repo.py scripts/rewrite_imports.py scripts/inject_smoke_test_cell.py scripts/edit_notebook_markdown.py: passed.
  • Notebook JSON parse across notebooks/**/*.ipynb: parsed 51 notebooks; 29 active, 22 archived, and 0 active top-level metadata.papermill entries after cleanup.
  • git submodule status --recursive: vendor/genai-vanilla now points to 0e4e9643ac273c6f36f815a5f4b3b187876bac74.
  • Verified pinned genai-vanilla JupyterHub content: services/jupyterhub/build/requirements.txt contains thekaveh-nnx[lm]==0.2.0, python-louvain, nltk, spacy, torchao>=0.17, and prettytable; services/jupyterhub/build/Dockerfile downloads en_core_web_sm and vader_lexicon.
  • YAML parse: .github/workflows/ci.yml, .github/workflows/pages.yml, deploy/genai-vanilla-jupyterhub.override.yml, and vendor/genai-vanilla/services/jupyterhub/compose.yml parsed successfully.
  • docker compose config --services with the wrapper env was attempted from vendor/genai-vanilla; full-stack config is blocked without genai-vanilla's generated .env and failed before a useful wrapper verdict. The JupyterHub fragment/override YAML and exact pinned runtime files were verified instead.
  • Live wiki probe: the GitHub wiki now contains the current ml-eng-lab signpost and planned Pages URL, so OM-011 was narrowed to Pages/default-branch/About drift.
  • curl -I -L https://thekaveh.github.io/ml-eng-lab/: still returned HTTP 404, matching deferred OM-011.
  • gh repo view thekaveh/ml-eng-lab --json name,description,homepageUrl,repositoryTopics,defaultBranchRef,url: default branch main, description/topics current, homepage still README pending live Pages.
  • git ls-remote https://github.com/thekaveh/genai-vanilla.git refs/heads/main: upstream main advanced to 675f1fffaf467a1f17ddd346e8b16fc6cbc365e0.
  • git -C vendor/genai-vanilla checkout 675f1fffaf467a1f17ddd346e8b16fc6cbc365e0: bumped the working submodule to the current upstream commit.
  • Verified pinned genai-vanilla JupyterHub content at 675f1fff: services/jupyterhub/build/requirements.txt still contains thekaveh-nnx[lm]==0.2.0, python-louvain, nltk, spacy, torchao>=0.17, and prettytable; services/jupyterhub/build/Dockerfile still downloads en_core_web_sm and vader_lexicon.
  • pytest tests/nnx_surface/test_notebook_api_surface.py::test_archive_cross_language_notebooks_guard_missing_model_artifacts -q: passed (1 passed, 3 warnings), covering missing-artifact guards in all 10 archived CodeXGLUE cross-language notebooks.
  • Notebook JSON parse across notebooks/**/*.ipynb: parsed 51 notebooks with 0 errors after archive guard edits.
  • Ignored local artifact cleanup: removed stale root-* duplicate run directories from notebooks/text_generation-tinyshakespeare-transformer-pytorch/runs/ and notebooks/preference_alignment-toy-dpo-pytorch/runs/, plus notebooks/image_classification-mnist-ffnn-numpy/__pycache__/; canonical non-root-* run dirs and runs/best remain.
  • rg -n "0e4e9643|cbad341|nnx-pytorch|675f1fff|675f1ff" README.md CONTRIBUTING.md docs notebooks ...: only current 675f1fff references and intentional historical migration notes remain.
  • python scripts/verify_repo.py --check all --fast: 0 errors, 4 known warnings for runtime-container-only torch_sparse imports in Reddit phase3 notebooks.
  • ruff check . --no-cache: passed.
  • make docs-build: passed with the upstream Material for MkDocs 2.0 warning.
  • pytest tests/ -v: 391 passed, 3 skipped, 17 warnings.
  • shellcheck scripts/start-jupyterhub.sh && bash -n scripts/start-jupyterhub.sh && sh -n vendor/genai-vanilla/start.sh && sh -n vendor/genai-vanilla/stop.sh: passed.
  • python -m py_compile scripts/verify_repo.py scripts/rewrite_imports.py scripts/inject_smoke_test_cell.py scripts/edit_notebook_markdown.py: passed.
  • git diff --check: passed.
  • pip-audit -r requirements.txt -r torch-requirements.txt: still reports the same 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • curl -I -L https://thekaveh.github.io/ml-eng-lab/: still returned HTTP 404, matching deferred OM-011.
  • gh repo view thekaveh/ml-eng-lab --json name,description,homepageUrl,repositoryTopics,defaultBranchRef,url: default branch main, description/topics current, homepage still README pending live Pages.
  • gh run list --repo thekaveh/ml-eng-lab --branch codex/overnight-maintenance --limit 5 --json ...: latest branch CI run remains the older failed 2df1c9b... run, matching deferred OM-012.
  • git ls-remote https://github.com/thekaveh/genai-vanilla.git refs/heads/main: upstream main advanced to d22014078041e59d076059a7704d265c79a777df.
  • git -C vendor/genai-vanilla checkout d22014078041e59d076059a7704d265c79a777df: bumped the working submodule to the current upstream commit.
  • Verified pinned genai-vanilla JupyterHub content at d2201407: services/jupyterhub/build/requirements.txt still contains thekaveh-nnx[lm]==0.2.0, python-louvain, nltk, spacy, torchao>=0.17, and prettytable; services/jupyterhub/build/Dockerfile still downloads en_core_web_sm and vader_lexicon.
  • pytest tests/nnx_surface/test_notebook_api_surface.py::test_archive_roberta_notebooks_require_explicit_rerun_opt_in -q: failed before the archived RoBERTa notebooks required explicit rerun opt-in, then passed after the notebook guard edits.
  • Focused archive regressions: pytest tests/nnx_surface/test_notebook_api_surface.py::test_archive_cross_language_notebooks_guard_missing_model_artifacts tests/nnx_surface/test_notebook_api_surface.py::test_archive_roberta_notebooks_require_explicit_rerun_opt_in tests/nnx_surface/test_notebook_api_surface.py::test_archive_notebook_guards_use_git_tracked_files -q passed (3 passed, 3 warnings).
  • python scripts/verify_repo.py --check all --fast: 0 errors, 4 known warnings for runtime-container-only torch_sparse imports in Reddit phase3 notebooks.
  • ruff check . --no-cache: passed.
  • make docs-build: passed with the upstream Material for MkDocs 2.0 warning.
  • shellcheck scripts/start-jupyterhub.sh && bash -n scripts/start-jupyterhub.sh && sh -n vendor/genai-vanilla/start.sh && sh -n vendor/genai-vanilla/stop.sh: passed.
  • python -m py_compile scripts/verify_repo.py scripts/rewrite_imports.py scripts/inject_smoke_test_cell.py scripts/edit_notebook_markdown.py: passed.
  • Notebook JSON parse across notebooks/**/*.ipynb: parsed 51 notebooks with 0 errors after archive guard edits.
  • First pass-8 pytest tests/ -v: failed in tests/test_verify_repo.py::test_run_helper_supplies_default_timeout because the cleaned fake subprocess callback no longer accepted subprocess.run keyword arguments.
  • pytest tests/test_verify_repo.py::test_run_helper_supplies_default_timeout -q: passed after restoring keyword-compatible fake arguments and explicitly discarding unused values inside the fake.
  • Final pass-8 pytest tests/ -v: 393 passed, 3 skipped, 17 warnings.
  • pip-audit -r requirements.txt -r torch-requirements.txt: still reports the same 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • git diff --check: passed.
  • make check-tier-a-clean: passed; active Tier-A notebooks remained unchanged by the archive-only notebook edits.
  • git ls-remote https://github.com/thekaveh/genai-vanilla.git refs/heads/main: upstream main remains d22014078041e59d076059a7704d265c79a777df, matching the pinned submodule.
  • curl -I -L https://thekaveh.github.io/ml-eng-lab/: still returned HTTP 404, matching deferred OM-011.
  • gh repo view thekaveh/ml-eng-lab --json name,description,homepageUrl,repositoryTopics,defaultBranchRef,url: default branch main, description/topics current, homepage still README pending live Pages.
  • gh run list --repo thekaveh/ml-eng-lab --branch codex/overnight-maintenance --limit 5 --json ...: latest branch CI run remains the older failed 2df1c9b... run, matching deferred OM-012.
  • git status --short --ignored=matching docs/superpowers and git check-ignore -v docs/superpowers/...: confirmed the stale docs/superpowers/** references are ignored local scratch files, not tracked repository docs.
  • pytest tests/nnx_surface/test_notebook_api_surface.py::test_archive_roberta_notebooks_require_explicit_rerun_opt_in -q: failed before guarding RoBERTa helper-copy setup and removing preprocessing os.chdir, then passed after the notebook updates.
  • pytest tests/test_verify_repo.py::test_structure_s2_checks_every_module_in_multi_import -q: failed before AST-backed import extraction, then passed after S2 began checking every alias in import a, b.
  • pytest tests/test_verify_repo.py tests/nnx_surface/test_notebook_api_surface.py -q: 355 passed, 3 warnings.
  • python scripts/verify_repo.py --check all --fast: 0 errors, 4 known warnings for runtime-container-only torch_sparse imports in Reddit phase3 notebooks.
  • ruff check . --no-cache: passed.
  • Notebook JSON parse across notebooks/**/*.ipynb: parsed 51 notebooks with 0 errors after pass-9 notebook edits.
  • Final pass-9 pytest tests/ -v: 394 passed, 3 skipped, 17 warnings.
  • pip-audit -r requirements.txt -r torch-requirements.txt: still reports the same 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • shellcheck scripts/start-jupyterhub.sh && bash -n scripts/start-jupyterhub.sh && sh -n vendor/genai-vanilla/start.sh && sh -n vendor/genai-vanilla/stop.sh: passed.
  • python -m py_compile scripts/verify_repo.py scripts/rewrite_imports.py scripts/inject_smoke_test_cell.py scripts/edit_notebook_markdown.py: passed.
  • git diff --check: passed.
  • make check-tier-a-clean: passed.
  • git ls-remote https://github.com/thekaveh/genai-vanilla.git refs/heads/main: upstream main advanced to d8ddd8e527c21ccbe78b34d72e2bb59409e52c6b.
  • git -C vendor/genai-vanilla checkout d8ddd8e527c21ccbe78b34d72e2bb59409e52c6b: bumped the working submodule to the current upstream commit.
  • Verified pinned genai-vanilla JupyterHub content at d8ddd8e: services/jupyterhub/build/requirements.txt still contains thekaveh-nnx[lm]==0.2.0, python-louvain, nltk, spacy, torchao>=0.17, and prettytable; services/jupyterhub/build/Dockerfile still downloads en_core_web_sm and vader_lexicon.
  • pytest tests/test_verify_repo.py::test_structure_s2_checks_multi_import_after_notebook_magic -q: failed before S2 handled notebook magic plus comma imports, then passed after notebook-only magic/shell lines were filtered and fallback import lines were parsed with AST.
  • pytest tests/test_verify_repo.py::test_structure_s2_checks_multi_import_after_notebook_magic tests/test_verify_repo.py::test_structure_s2_checks_every_module_in_multi_import -q: 2 passed.
  • python scripts/verify_repo.py --check all --fast: 0 errors, 4 known warnings for runtime-container-only torch_sparse imports in Reddit phase3 notebooks.
  • ruff check scripts/verify_repo.py tests/test_verify_repo.py --no-cache: passed.
  • ruff check . --no-cache: passed.
  • make docs-build: passed with the known MkDocs/Material warning.
  • shellcheck scripts/start-jupyterhub.sh && bash -n scripts/start-jupyterhub.sh && sh -n vendor/genai-vanilla/start.sh && sh -n vendor/genai-vanilla/stop.sh: passed.
  • python -m py_compile scripts/verify_repo.py scripts/rewrite_imports.py scripts/inject_smoke_test_cell.py scripts/edit_notebook_markdown.py: passed.
  • Notebook JSON parse across notebooks/**/*.ipynb: parsed 51 notebooks with 0 errors.
  • git diff --check && make check-tier-a-clean: passed.
  • pip-audit -r requirements.txt -r torch-requirements.txt: still reports the same 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • Final pass-10 pytest tests/ -v: 395 passed, 3 skipped, 17 warnings.
  • pytest tests/test_verify_repo.py::test_structure_s2_ignores_non_python_cell_magic_body tests/test_verify_repo.py::test_structure_s2_flags_notebook_relative_imports -q: failed before S2 skipped non-Python cell-magic bodies and reported notebook-relative imports explicitly.
  • pytest tests/test_verify_repo.py::test_structure_s2_ignores_non_python_cell_magic_body tests/test_verify_repo.py::test_structure_s2_flags_notebook_relative_imports tests/test_verify_repo.py::test_structure_s2_checks_multi_import_after_notebook_magic tests/test_verify_repo.py::test_structure_s2_checks_every_module_in_multi_import -q: 4 passed.
  • git ls-remote https://github.com/thekaveh/genai-vanilla.git refs/heads/main: upstream main remained at d8ddd8e527c21ccbe78b34d72e2bb59409e52c6b, matching the superproject gitlink.
  • Final pass-11 pytest tests/ -v: 397 passed, 3 skipped, 17 warnings.
  • git ls-remote https://github.com/thekaveh/genai-vanilla.git refs/heads/main: upstream main advanced to 2bee05134d721a152a6ea579d9a65efd7e080701.
  • git -C vendor/genai-vanilla checkout 2bee05134d721a152a6ea579d9a65efd7e080701: bumped the working submodule to the current upstream commit.
  • Verified pinned genai-vanilla JupyterHub content at 2bee051: services/jupyterhub/build/requirements.txt still contains thekaveh-nnx[lm]==0.2.0, python-louvain, nltk, spacy, torchao>=0.17, and prettytable; services/jupyterhub/build/Dockerfile still downloads en_core_web_sm and vader_lexicon.
  • git ls-remote https://github.com/thekaveh/genai-vanilla.git refs/heads/main: upstream main advanced to a22b182a0f0cd1bb0be3599a7710d87890491eb8.
  • git -C vendor/genai-vanilla checkout a22b182a0f0cd1bb0be3599a7710d87890491eb8: bumped the working submodule to the current upstream commit.
  • git -C vendor/genai-vanilla diff --name-status 2bee05134d721a152a6ea579d9a65efd7e080701..a22b182a0f0cd1bb0be3599a7710d87890491eb8: upstream delta is Browserless research docs and a bootstrapper test; no JupyterHub runtime files changed.
  • Verified pinned genai-vanilla JupyterHub content at a22b182: services/jupyterhub/build/requirements.txt still contains thekaveh-nnx[lm]==0.2.0, python-louvain, nltk, spacy, torchao>=0.17, and prettytable; services/jupyterhub/build/Dockerfile still downloads en_core_web_sm and vader_lexicon.
  • pytest tests/test_verify_repo.py::test_e6_shellcheck_targets_include_consumed_vendor_entrypoints -q: failed before _shellcheck_targets included the consumed JupyterHub image startup.sh, then passed after the target was added.
  • pytest tests/test_verify_repo.py::test_structure_s2_flags_dotted_notebook_relative_imports -q: failed before S2 treated dotted from .helpers import ... as a relative import.
  • pytest tests/test_verify_repo.py::test_structure_s2_checks_every_module_in_multi_import tests/test_verify_repo.py::test_structure_s2_checks_multi_import_after_notebook_magic tests/test_verify_repo.py::test_structure_s2_ignores_non_python_cell_magic_body tests/test_verify_repo.py::test_structure_s2_flags_notebook_relative_imports tests/test_verify_repo.py::test_structure_s2_flags_dotted_notebook_relative_imports -q: 5 passed.
  • pytest tests/test_verify_repo.py::test_e6_shellcheck_targets_include_consumed_vendor_entrypoints -q: failed before _shellcheck_targets included vendor/genai-vanilla/start.sh and vendor/genai-vanilla/stop.sh, then passed after the target helper was added.
  • python scripts/verify_repo.py --check execution --fast: 0 findings after extending E6 shellcheck targets.
  • Final pass-12 pytest tests/ -v: 399 passed, 3 skipped, 17 warnings.
  • pytest tests/test_verify_repo.py::test_structure_s2_reports_one_based_line_numbers tests/test_verify_repo.py::test_structure_s2_dedupe_does_not_hide_relative_imports tests/test_verify_repo.py::test_structure_s2_fallback_ignores_multiline_string_import_text -q: all 3 tests failed before the pass-13 S2 fixes.
  • pytest tests/test_verify_repo.py::test_structure_s2_reports_one_based_line_numbers tests/test_verify_repo.py::test_structure_s2_dedupe_does_not_hide_relative_imports tests/test_verify_repo.py::test_structure_s2_fallback_ignores_multiline_string_import_text tests/test_verify_repo.py::test_structure_s2_checks_every_module_in_multi_import tests/test_verify_repo.py::test_structure_s2_checks_multi_import_after_notebook_magic tests/test_verify_repo.py::test_structure_s2_ignores_non_python_cell_magic_body tests/test_verify_repo.py::test_structure_s2_flags_notebook_relative_imports tests/test_verify_repo.py::test_structure_s2_flags_dotted_notebook_relative_imports -q: 8 passed.
  • pytest tests/test_verify_repo.py::test_e6_shellcheck_targets_include_consumed_vendor_entrypoints -q: failed before _shellcheck_targets included vendor/genai-vanilla/bootstrapper/_run.sh, then passed after the dispatcher target was added.
  • python scripts/verify_repo.py --check execution --fast: 0 findings after extending E6 shellcheck targets to the vendor dispatcher.
  • Final pass-13 pytest tests/ -v: 402 passed, 3 skipped, 17 warnings.
  • Pass 17 focused E6 regressions: pytest tests/test_verify_repo.py::test_e6_flags_missing_required_vendor_shellcheck_targets tests/test_verify_repo.py::test_e6_flags_missing_required_vendor_shellcheck_targets_without_shellcheck tests/test_verify_repo.py::test_e6_shellcheck_targets_include_consumed_vendor_entrypoints -q: 3 passed.
  • python scripts/verify_repo.py --check all --fast: 0 findings.
  • python -m pytest --collect-only -q -p no:cacheprovider: 409 tests collected.
  • ruff check . --no-cache: passed.
  • make docs-build: passed with the known MkDocs/Material warning.
  • Shellcheck/syntax over scripts/start-jupyterhub.sh, vendor/genai-vanilla/start.sh, vendor/genai-vanilla/stop.sh, vendor/genai-vanilla/bootstrapper/_run.sh, and vendor/genai-vanilla/services/jupyterhub/build/scripts/startup.sh: passed.
  • python -m py_compile scripts/verify_repo.py scripts/rewrite_imports.py scripts/inject_smoke_test_cell.py scripts/edit_notebook_markdown.py: passed.
  • YAML parse: .github/workflows/ci.yml, .github/workflows/pages.yml, deploy/genai-vanilla-jupyterhub.override.yml, and vendor/genai-vanilla/services/jupyterhub/compose.yml parsed successfully.
  • Notebook JSON parse across notebooks/**/*.ipynb: parsed 51 notebooks.
  • git diff --check && make check-tier-a-clean: passed.
  • pip-audit -r docs-requirements.txt: no known vulnerabilities found.
  • pip-audit -r requirements.txt -r torch-requirements.txt: still reports the same 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • Final pass-17 pytest tests/ -v: 406 passed, 3 skipped, 17 warnings.
  • Pass 18 red/green verifier config regression: pytest tests/test_verify_repo.py::test_repo_root_uses_target_repo_config_for_active_dirs -q failed before --repo-root honored a target repo's own scripts/verify_repo_config.yaml, then passed after the config activation fix.
  • Pass 18 red/green rewrite regression: pytest tests/test_rewrite_imports.py::test_parenthesized_graph_att_params_import_with_inline_comment -q failed before inline-comment import members were normalized, then passed after the parser fix.
  • Pass 18 red/green archive regressions: pytest tests/nnx_surface/test_notebook_api_surface.py::test_archive_cross_language_notebooks_require_explicit_rerun_opt_in tests/nnx_surface/test_notebook_api_surface.py::test_archive_notebooks_do_not_depend_on_kernel_cwd -q failed before adding cross-language rerun gates and archive-folder anchoring, then passed after the notebook edits.
  • Focused affected suites: pytest tests/test_verify_repo.py tests/test_rewrite_imports.py -q passed (86 passed); archive guard group passed (5 passed, 3 warnings).
  • git ls-remote https://github.com/thekaveh/genai-vanilla.git refs/heads/main: upstream main advanced to 0bc3abd3cafb35b340f90c4efa89d64375ac9152; git -C vendor/genai-vanilla diff --name-status 448333d3b1a530fafd76d224ee1066181de8fac4..0bc3abd3cafb35b340f90c4efa89d64375ac9152 showed only OpenLIT research docs/tests, with no JupyterHub runtime-file changes.
  • Verified pinned genai-vanilla JupyterHub content at 0bc3abd: services/jupyterhub/build/requirements.txt still contains thekaveh-nnx[lm]==0.2.0, python-louvain, nltk, spacy, torchao>=0.17, and prettytable; services/jupyterhub/build/Dockerfile still downloads en_core_web_sm and vader_lexicon.
  • python scripts/verify_repo.py --check all --fast: 0 findings.
  • python -m pytest --collect-only -q -p no:cacheprovider: 413 tests collected.
  • ruff check . --no-cache: passed.
  • make docs-build: passed with the known MkDocs/Material warning.
  • Shellcheck/syntax over scripts/start-jupyterhub.sh, vendor/genai-vanilla/start.sh, vendor/genai-vanilla/stop.sh, vendor/genai-vanilla/bootstrapper/_run.sh, and vendor/genai-vanilla/services/jupyterhub/build/scripts/startup.sh: passed.
  • python -m py_compile scripts/verify_repo.py scripts/rewrite_imports.py scripts/inject_smoke_test_cell.py scripts/edit_notebook_markdown.py: passed.
  • YAML parse: .github/workflows/ci.yml, .github/workflows/pages.yml, scripts/verify_repo_config.yaml, mkdocs.yml, deploy/genai-vanilla-jupyterhub.override.yml, and vendor/genai-vanilla/services/jupyterhub/compose.yml parsed successfully.
  • Notebook JSON parse across notebooks/**/*.ipynb: parsed 51 notebooks.
  • git diff --check && make check-tier-a-clean: passed.
  • pip-audit -r docs-requirements.txt: no known vulnerabilities found.
  • pip-audit -r requirements.txt -r torch-requirements.txt: still reports the same 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • Final pass-18 pytest tests/ -v: 410 passed, 3 skipped, 17 warnings.
  • Pass 19 red/green rewrite regressions: pytest tests/test_rewrite_imports.py::test_parenthesized_graph_att_params_import_with_closing_paren_same_line tests/test_rewrite_imports.py::test_common_nn_model_split_import_with_inline_comment -q passed after the rewriter stripped deprecated params before same-line closing parens and split inline-commented common.nn_model imports.
  • Pass 19 red/green S2 regression: pytest tests/test_verify_repo.py::test_structure_s2_checks_literal_dynamic_imports -q passed after _imported_modules_from_source started yielding literal importlib.import_module(...) and __import__(...) calls.
  • Pass 19 active notebook metadata scan: 29 active notebooks checked, 0 kernelspec/language-version mismatches after normalization to python3 / Python 3.11 metadata.
  • Pass 19 affected verifier/rewrite suite: pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed (89 passed).
  • git ls-remote https://github.com/thekaveh/genai-vanilla.git refs/heads/main: upstream main advanced to 2997143758f58f4c40ecd6e258fa8422942cb7cd; git -C vendor/genai-vanilla diff --name-status 0bc3abd3cafb35b340f90c4efa89d64375ac9152..2997143758f58f4c40ecd6e258fa8422942cb7cd showed only live-trading research docs/tests, with no JupyterHub runtime-file changes.
  • Verified pinned genai-vanilla JupyterHub content at 2997143: services/jupyterhub/build/requirements.txt still contains thekaveh-nnx[lm]==0.2.0, python-louvain, nltk, spacy, torchao>=0.17, and prettytable; services/jupyterhub/build/Dockerfile still downloads en_core_web_sm and vader_lexicon.
  • python scripts/verify_repo.py --check all --fast: 0 findings.
  • python -m pytest --collect-only -q -p no:cacheprovider: 416 tests collected.
  • ruff check . --no-cache: passed.
  • make docs-build: passed with the known MkDocs/Material warning.
  • Shellcheck/syntax over scripts/start-jupyterhub.sh, vendor/genai-vanilla/start.sh, vendor/genai-vanilla/stop.sh, vendor/genai-vanilla/bootstrapper/_run.sh, and vendor/genai-vanilla/services/jupyterhub/build/scripts/startup.sh: passed.
  • python -m py_compile scripts/verify_repo.py scripts/rewrite_imports.py scripts/inject_smoke_test_cell.py scripts/edit_notebook_markdown.py: passed.
  • YAML parse: .github/workflows/ci.yml, .github/workflows/pages.yml, scripts/verify_repo_config.yaml, mkdocs.yml, deploy/genai-vanilla-jupyterhub.override.yml, and vendor/genai-vanilla/services/jupyterhub/compose.yml parsed successfully.
  • Notebook JSON parse across notebooks/**/*.ipynb: parsed 51 notebooks.
  • git diff --check: passed.
  • Staged make check-tier-a-clean: passed for the intentional active-notebook metadata edits.
  • pip-audit -r docs-requirements.txt: no known vulnerabilities found.
  • pip-audit -r requirements.txt -r torch-requirements.txt: still reports the same 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • Final pass-19 pytest tests/ -v: 413 passed, 3 skipped, 17 warnings.
  • Pass 20 red/green rewrite regressions: pytest tests/test_rewrite_imports.py::test_single_line_parenthesized_params_import_is_preserved_and_rewritten tests/test_rewrite_imports.py::test_single_line_parenthesized_params_only_import_drops_empty_import -q failed before same-line parenthesized imports were normalized, then passed after the fix.
  • Pass 20 red/green S2 regression: pytest tests/test_verify_repo.py::test_structure_s2_checks_literal_dynamic_import_aliases -q failed before importlib alias tracking, then passed after _imported_modules_from_source recognized from importlib import import_module and import importlib as il.
  • Pass 20 local ignored-doc link checker over docs/superpowers/plans/*.md: 53 broken local links before mechanical path cleanup, 0 after. These files remain ignored scratch docs and were not force-added to the branch.
  • Pass 20 affected verifier/rewrite suite: pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed (92 passed).
  • python scripts/verify_repo.py --check all --fast: 0 findings.
  • python -m pytest --collect-only -q -p no:cacheprovider: 419 tests collected.
  • ruff check . --no-cache: passed.
  • make docs-build: passed with the known MkDocs/Material warning.
  • Shellcheck/syntax over scripts/start-jupyterhub.sh, vendor/genai-vanilla/start.sh, vendor/genai-vanilla/stop.sh, vendor/genai-vanilla/bootstrapper/_run.sh, and vendor/genai-vanilla/services/jupyterhub/build/scripts/startup.sh: passed.
  • python -m py_compile scripts/verify_repo.py scripts/rewrite_imports.py scripts/inject_smoke_test_cell.py scripts/edit_notebook_markdown.py: passed.
  • YAML parse: .github/workflows/ci.yml, .github/workflows/pages.yml, scripts/verify_repo_config.yaml, mkdocs.yml, deploy/genai-vanilla-jupyterhub.override.yml, and vendor/genai-vanilla/services/jupyterhub/compose.yml parsed successfully.
  • Notebook JSON parse across notebooks/**/*.ipynb: parsed 51 notebooks.
  • make check-tier-a-clean && git diff --check: passed.
  • pip-audit -r docs-requirements.txt: no known vulnerabilities found.
  • pip-audit -r requirements.txt -r torch-requirements.txt: still reports the same 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • Final pass-20 pytest tests/ -v: 416 passed, 3 skipped, 17 warnings.
  • Pass 21 red/green rewrite regression: pytest tests/test_rewrite_imports.py::test_multiline_source_chunk_is_split_before_rewriting -q failed before notebook list-source chunks were split into physical lines, then passed after process_notebook normalized chunks with splitlines(keepends=True).
  • Pass 21 red/green verifier regressions: pytest tests/test_verify_repo.py::test_structure_s2_fallback_checks_literal_dynamic_import_aliases tests/test_verify_repo.py::test_e6_flags_dirty_required_submodule -q failed before S2 fallback alias tracking and required-submodule dirty detection, then passed after the verifier fixes.
  • Pass 21 affected verifier/rewrite suite: pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed (95 passed).
  • git -C vendor/genai-vanilla diff --name-status 2997143758f58f4c40ecd6e258fa8422942cb7cd..163134451a19d024e0e1c0df51139fd8c0a2ca52: upstream delta adds FinRL FinGPT research docs/tests only; JupyterHub runtime files are unchanged.
  • Verified pinned genai-vanilla JupyterHub content at 1631344: services/jupyterhub/build/requirements.txt still contains thekaveh-nnx[lm]==0.2.0, python-louvain, nltk, spacy, torchao>=0.17, and prettytable; services/jupyterhub/build/Dockerfile still downloads en_core_web_sm and vader_lexicon.
  • python scripts/verify_repo.py --check all --fast: 0 findings.
  • git submodule status vendor/genai-vanilla: clean 163134451a19d024e0e1c0df51139fd8c0a2ca52 vendor/genai-vanilla.
  • git diff --cached --submodule=log -- vendor/genai-vanilla: 2997143..1631344 with Capture FinRL FinGPT notebook deferral (#302).
  • python -m pytest --collect-only -q -p no:cacheprovider: 422 tests collected.
  • ruff check . --no-cache: passed.
  • make docs-build: passed with the known MkDocs/Material warning.
  • Shellcheck/syntax over scripts/start-jupyterhub.sh, vendor/genai-vanilla/start.sh, vendor/genai-vanilla/stop.sh, vendor/genai-vanilla/bootstrapper/_run.sh, and vendor/genai-vanilla/services/jupyterhub/build/scripts/startup.sh: passed.
  • python -m py_compile scripts/verify_repo.py scripts/rewrite_imports.py scripts/inject_smoke_test_cell.py scripts/edit_notebook_markdown.py: passed.
  • YAML parse: .github/workflows/ci.yml, .github/workflows/pages.yml, scripts/verify_repo_config.yaml, mkdocs.yml, deploy/genai-vanilla-jupyterhub.override.yml, and vendor/genai-vanilla/services/jupyterhub/compose.yml parsed successfully.
  • Notebook JSON parse across notebooks/**/*.ipynb: parsed 51 notebooks.
  • git diff --cached --check && git diff --check: passed.
  • make check-tier-a-clean: passed.
  • pip-audit -r docs-requirements.txt: no known vulnerabilities found.
  • pip-audit -r requirements.txt -r torch-requirements.txt: still reports the same 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • Final pass-21 pytest tests/ -v: 419 passed, 3 skipped, 17 warnings.
  • Pass 22 red/green verifier regressions: pytest tests/test_verify_repo.py::test_structure_s2_fallback_checks_multiline_literal_dynamic_import_aliases tests/test_verify_repo.py::test_e6_flags_required_submodule_with_modified_worktree -q failed before multiline importlib-alias fallback parsing and required-submodule worktree checks, then passed after the verifier fixes.
  • Pass 22 red/green rewrite regression: pytest tests/test_rewrite_imports.py::test_source_chunks_are_joined_before_rewriting_logical_lines -q failed before source-list chunks were joined into logical source before line splitting, then passed after the process_notebook fix.
  • Pass 22 affected verifier/rewrite suite: pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed (98 passed).
  • python -m py_compile scripts/verify_repo.py scripts/rewrite_imports.py: passed.
  • python scripts/verify_repo.py --check all --fast: 0 findings.
  • python -m pytest --collect-only -q -p no:cacheprovider: 425 tests collected.
  • ruff check . --no-cache: passed.
  • make docs-build: passed with the known MkDocs/Material warning.
  • Shellcheck/syntax over scripts/start-jupyterhub.sh, vendor/genai-vanilla/start.sh, vendor/genai-vanilla/stop.sh, vendor/genai-vanilla/bootstrapper/_run.sh, and vendor/genai-vanilla/services/jupyterhub/build/scripts/startup.sh: passed.
  • YAML parse: .github/workflows/ci.yml, .github/workflows/pages.yml, scripts/verify_repo_config.yaml, mkdocs.yml, deploy/genai-vanilla-jupyterhub.override.yml, and vendor/genai-vanilla/services/jupyterhub/compose.yml parsed successfully.
  • Notebook JSON parse across notebooks/**/*.ipynb: parsed 51 notebooks.
  • git diff --check: passed.
  • make check-tier-a-clean: passed.
  • pip-audit -r docs-requirements.txt: no known vulnerabilities found.
  • pip-audit -r requirements.txt -r torch-requirements.txt: still reports the same 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • Final pass-22 pytest tests/ -v: 422 passed, 3 skipped, 17 warnings.
  • Pass 23 genai-vanilla upstream check: upstream main advanced from 163134451a19d024e0e1c0df51139fd8c0a2ca52 to b96a2924b5d30aa30eddb2fa43f9b7a47fc81bcb; git -C vendor/genai-vanilla diff --name-status 163134451a19d024e0e1c0df51139fd8c0a2ca52..b96a2924b5d30aa30eddb2fa43f9b7a47fc81bcb showed heavy 3D infrastructure research docs/tests only.
  • Verified pinned genai-vanilla JupyterHub content at b96a292: services/jupyterhub/build/requirements.txt still contains thekaveh-nnx[lm]==0.2.0, python-louvain, nltk, spacy, torchao>=0.17, and prettytable; services/jupyterhub/build/Dockerfile still downloads en_core_web_sm and vader_lexicon.
  • Pass 23 red/green verifier regressions: pytest tests/test_verify_repo.py::test_structure_s2_fallback_checks_multiline_literal_dynamic_import_calls tests/test_verify_repo.py::test_docs_d10_flags_dependency_ledger_submodule_sha_drift tests/test_verify_repo.py::test_e6_flags_required_submodule_with_modified_worktree -q failed the first two tests before multiline dynamic-call fallback parsing and ledger-vs-gitlink verification, while the cwd coverage guard already passed against the current implementation; all three passed after fixes.
  • Pass 23 affected verifier/rewrite suite: pytest tests/test_verify_repo.py tests/test_rewrite_imports.py -q passed (100 passed).
  • python scripts/verify_repo.py --check all --fast: 0 findings after staging the vendor/genai-vanilla gitlink at b96a292.
  • git submodule status vendor/genai-vanilla: clean b96a2924b5d30aa30eddb2fa43f9b7a47fc81bcb vendor/genai-vanilla.
  • git diff --cached --submodule=log -- vendor/genai-vanilla: 1631344..b96a292 with Capture heavy 3D infrastructure deferral (#303).
  • python -m pytest --collect-only -q -p no:cacheprovider: 427 tests collected.
  • ruff check . --no-cache: passed.
  • make docs-build: passed with the known MkDocs/Material warning.
  • Shellcheck/syntax over scripts/start-jupyterhub.sh, vendor/genai-vanilla/start.sh, vendor/genai-vanilla/stop.sh, vendor/genai-vanilla/bootstrapper/_run.sh, and vendor/genai-vanilla/services/jupyterhub/build/scripts/startup.sh: passed.
  • python -m py_compile scripts/verify_repo.py scripts/rewrite_imports.py scripts/inject_smoke_test_cell.py scripts/edit_notebook_markdown.py: passed.
  • YAML parse: .github/workflows/ci.yml, .github/workflows/pages.yml, scripts/verify_repo_config.yaml, mkdocs.yml, deploy/genai-vanilla-jupyterhub.override.yml, and vendor/genai-vanilla/services/jupyterhub/compose.yml parsed successfully.
  • Notebook JSON parse across notebooks/**/*.ipynb: parsed 51 notebooks.
  • git diff --cached --check && git diff --check: passed.
  • make check-tier-a-clean: passed.
  • pip-audit -r docs-requirements.txt: no known vulnerabilities found.
  • pip-audit -r requirements.txt -r torch-requirements.txt: still reports the same 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • Final pass-23 pytest tests/ -v: 424 passed, 3 skipped, 17 warnings.
  • Pass 24 genai-vanilla upstream check: upstream main advanced from b96a2924b5d30aa30eddb2fa43f9b7a47fc81bcb to ba21661e8a63b3727b9c4a14eaf5e61262d4b48e; git -C vendor/genai-vanilla diff --name-status b96a2924b5d30aa30eddb2fa43f9b7a47fc81bcb..ba21661e8a63b3727b9c4a14eaf5e61262d4b48e showed voice-stack research docs/tests only.
  • Verified pinned genai-vanilla JupyterHub content at ba21661: services/jupyterhub/build/requirements.txt still contains thekaveh-nnx[lm]==0.2.0, python-louvain, nltk, spacy, torchao>=0.17, and prettytable; services/jupyterhub/build/Dockerfile still downloads en_core_web_sm and vader_lexicon.
  • Pass 24 red/green verifier regressions: pytest tests/test_verify_repo.py::test_structure_s2_fallback_checks_backslash_continued_multi_imports tests/test_verify_repo.py::test_docs_d10_flags_missing_dependency_ledger_submodule_sha -q failed before S2 backslash-continuation reconstruction and D10 fail-closed SHA parsing, then passed after the verifier fixes.
  • Pass 24 focused verifier regressions: pytest tests/test_verify_repo.py::test_structure_s2_fallback_checks_backslash_continued_multi_imports tests/test_verify_repo.py::test_docs_d10_flags_missing_dependency_ledger_submodule_sha tests/test_verify_repo.py::test_docs_d10_flags_dependency_ledger_submodule_sha_drift tests/test_verify_repo.py::test_structure_s2_fallback_checks_multiline_literal_dynamic_import_calls tests/test_verify_repo.py::test_structure_s2_fallback_checks_multiline_literal_dynamic_import_aliases -q passed (5 passed).
  • Pass 24 affected verifier/rewrite suite: pytest tests/test_verify_repo.py tests/test_rewrite_imports.py -q passed (102 passed).
  • python scripts/verify_repo.py --check all --fast: 0 findings after staging the vendor/genai-vanilla gitlink at ba21661.
  • git submodule status vendor/genai-vanilla: clean ba21661e8a63b3727b9c4a14eaf5e61262d4b48e vendor/genai-vanilla.
  • git diff --cached --submodule=log -- vendor/genai-vanilla: b96a292..ba21661 with Capture voice stack deferral decision (#304).
  • python -m pytest --collect-only -q -p no:cacheprovider: 429 tests collected.
  • ruff check . --no-cache: passed.
  • make docs-build: passed with the known MkDocs/Material warning.
  • Shellcheck/syntax over scripts/start-jupyterhub.sh, vendor/genai-vanilla/start.sh, vendor/genai-vanilla/stop.sh, vendor/genai-vanilla/bootstrapper/_run.sh, and vendor/genai-vanilla/services/jupyterhub/build/scripts/startup.sh: passed.
  • python -m py_compile scripts/verify_repo.py scripts/rewrite_imports.py scripts/inject_smoke_test_cell.py scripts/edit_notebook_markdown.py: passed.
  • YAML parse: .github/workflows/ci.yml, .github/workflows/pages.yml, scripts/verify_repo_config.yaml, mkdocs.yml, deploy/genai-vanilla-jupyterhub.override.yml, and vendor/genai-vanilla/services/jupyterhub/compose.yml parsed successfully.
  • Notebook JSON parse across notebooks/**/*.ipynb: parsed 51 notebooks.
  • git diff --cached --check && git diff --check: passed.
  • make check-tier-a-clean: passed.
  • pip-audit -r docs-requirements.txt: no known vulnerabilities found.
  • pip-audit -r requirements.txt -r torch-requirements.txt: still reports the same 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • Final pass-24 pytest tests/ -v: 426 passed, 3 skipped, 17 warnings.
  • Pass 25 subagent finding disposition: the stale ml-lab wording inside pinned genai-vanilla comments is the previously documented/deferred OM-053 vendor issue, not a new pass-25 issue; the PASSES=20 header is the configured consecutive-zero stop target, not the completed pass count, so it remains accurate.
  • Pass 25 red/green regressions: pytest tests/test_rewrite_imports.py::test_params_call_site_with_backslash_continuation_renamed_to_nnparams tests/test_verify_repo.py::test_docs_d10_flags_missing_dependency_ledger_gitlink -q failed before rewrite-import logical-continuation handling and D10 missing-gitlink reporting, then passed after fixes (2 passed).
  • Pass 25 affected verifier/rewrite suite: pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed (104 passed).
  • Pass 25 genai-vanilla upstream check: upstream main advanced from ba21661e8a63b3727b9c4a14eaf5e61262d4b48e to 329f883139f9b101ef923376b84d5d9199c47b56; git -C vendor/genai-vanilla diff --name-status ba21661e8a63b3727b9c4a14eaf5e61262d4b48e..329f883139f9b101ef923376b84d5d9199c47b56 showed Honcho research docs/tests only.
  • Verified pinned genai-vanilla JupyterHub content at 329f883: services/jupyterhub/build/requirements.txt still contains thekaveh-nnx[lm]==0.2.0, python-louvain, nltk, spacy, torchao>=0.17, and prettytable; services/jupyterhub/build/Dockerfile still downloads en_core_web_sm and vader_lexicon.
  • git submodule status vendor/genai-vanilla: clean 329f883139f9b101ef923376b84d5d9199c47b56 vendor/genai-vanilla.
  • git diff --cached --submodule=log -- vendor/genai-vanilla: ba21661..329f883 with Capture Honcho deferral decision (#305).
  • python scripts/verify_repo.py --check all --fast: 0 findings.
  • Pass 26 branch/upstream and submodule parity: git status --short --branch was clean, git rev-list --left-right --count @{u}...HEAD returned 0 0, and both git ls-remote https://github.com/thekaveh/genai-vanilla.git refs/heads/main and git submodule status vendor/genai-vanilla resolved to 329f883139f9b101ef923376b84d5d9199c47b56.
  • Pass 26 focused tooling regression suite: pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed (104 passed).
  • Pass 26 verifier: python scripts/verify_repo.py --check all --fast reported 0 findings.
  • Pass 26 docs reviewer evidence: docs verifier returned 0 findings; a local Markdown checker over 15 published/doc entry files found 79 internal links and 0 broken links; MkDocs nav had 13 entries and 0 missing targets; numbered-heading checker found 0 unnumbered non-H1 headings.
  • Pass 26 notebook reviewer evidence: parsed 51 tracked notebooks, counted 29 active and 22 archived notebooks, scanned all active notebooks for stale ml-lab URLs, old Jupyter/Codespaces/local paths, ../data, ../runs, %cd, and os.chdir with 0 hits, and confirmed archive rerun/path guards remain covered.
  • Pass 26 tooling reviewer evidence: pip-audit -r requirements.txt -r torch-requirements.txt still reported the ledgered 23 known vulnerabilities across torch, pytorch-lightning, and nltk; shellcheck and syntax checks passed for local and consumed vendor entrypoints; workflow uses: references remain pinned to 40-character SHAs.
  • Pass 26 Python reviewer evidence: pytest -q passed (428 passed, 3 skipped); python -m compileall -q scripts tests passed; radon cc -s -n B scripts/verify_repo.py scripts/rewrite_imports.py showed existing complexity hotspots but no reportable new blocking regression.
  • Pass 27 branch/upstream and submodule parity: git status --short --branch was clean, git rev-list --left-right --count @{u}...HEAD returned 0 0, and both git ls-remote https://github.com/thekaveh/genai-vanilla.git refs/heads/main and git submodule status vendor/genai-vanilla resolved to 329f883139f9b101ef923376b84d5d9199c47b56.
  • Pass 27 focused tooling regression suite: pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed (104 passed).
  • Pass 27 verifier: python scripts/verify_repo.py --check all --fast reported 0 findings.
  • Pass 27 docs reviewer evidence: mkdocs build --strict --site-dir /tmp/ml-lab-pass27-mkdocs --clean passed; docs and structure verifiers returned 0 findings; read-only Markdown/nav checker found 79 internal links and 0 broken links, 13 nav entries and 0 missing targets; numbered-heading checker found 0 issues.
  • Pass 27 notebook reviewer evidence: scanned 29 active notebooks with 0 stale repo names, stale pins, bad absolute repo paths, parent ../data/../runs, missing papermill parameter tags, or /tmp papermill metadata; sampled archive notebooks confirmed ARCHIVE_RERUN_ENABLED = False gates destructive/rebuild behavior.
  • Pass 27 tooling reviewer evidence: pip-audit -r requirements.txt -r torch-requirements.txt still reported the expected ledgered 23 known vulnerabilities; workflow uses: entries remain pinned to 40-character SHAs and match documented tags; shellcheck/syntax passed for local and consumed vendor entrypoints.
  • Pass 27 Python reviewer evidence: fallback import parsing, D10 ledger checks, and rewrite-import chunk/continuation behavior were reviewed; ruff check scripts/verify_repo.py scripts/rewrite_imports.py tests/test_verify_repo.py tests/test_rewrite_imports.py passed.
  • Pass 28 branch/upstream and submodule parity: git status --short --branch was clean, git rev-list --left-right --count @{u}...HEAD returned 0 0, and both git ls-remote https://github.com/thekaveh/genai-vanilla.git refs/heads/main and git submodule status vendor/genai-vanilla resolved to 329f883139f9b101ef923376b84d5d9199c47b56.
  • Pass 28 verifier: python scripts/verify_repo.py --check all --fast reported 0 findings before fixes.
  • Pass 28 pre-fix affected suite: pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed (104 passed) before the new regression was added.
  • Pass 28 red/green rewrite regression: pytest tests/test_rewrite_imports.py::test_nnparams_import_inserted_after_cell_magic -q failed before rewrite_imports.py preserved first-line %% cell magics during NNParams import injection, then passed after the fix.
  • Pass 28 affected verifier/rewrite suite: pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed (105 passed).
  • Pass 28 docs chronology repair: moved the pass-17/pass-18 validation evidence before pass 19, eliminating the adjacent pass-order drop from pass 27 back to pass 18 in the validation log.
  • Pass 28 final verifier: python scripts/verify_repo.py --check all --fast reported 0 findings after fixes.
  • Pass 28 final validation: ruff check . --no-cache, make docs-build, python -m py_compile scripts/verify_repo.py scripts/rewrite_imports.py scripts/inject_smoke_test_cell.py scripts/edit_notebook_markdown.py, and git diff --check passed.
  • Pass 28 full pytest: pytest tests/ -v passed (429 passed, 3 skipped, 17 warnings).
  • Pass 28 artifact validation: notebook JSON parse covered 51 notebooks; YAML parse covered .github/workflows/ci.yml, .github/workflows/pages.yml, scripts/verify_repo_config.yaml, mkdocs.yml, deploy/genai-vanilla-jupyterhub.override.yml, and vendor/genai-vanilla/services/jupyterhub/compose.yml; shellcheck/syntax passed for local and consumed vendor shell entrypoints.
  • Pass 28 audit validation: pip-audit -r docs-requirements.txt found no known vulnerabilities; pip-audit -r requirements.txt -r torch-requirements.txt still reported the ledgered 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • Pass 29 branch/upstream parity: git status --short --branch was clean at pass start, and git rev-list --left-right --count @{u}...HEAD returned 0 0.
  • Pass 29 genai-vanilla upstream check: upstream main advanced from 329f883139f9b101ef923376b84d5d9199c47b56 to c2ffe8d10f5f21c549b411d87861c83e518073ba; git -C vendor/genai-vanilla diff --name-status 329f883139f9b101ef923376b84d5d9199c47b56..c2ffe8d10f5f21c549b411d87861c83e518073ba showed Redis Stack/RedisInsight research docs and a bootstrapper deferral test only.
  • Pass 29 JupyterHub runtime contract check: at c2ffe8d, services/jupyterhub/build/requirements.txt still includes thekaveh-nnx[lm]==0.2.0, python-louvain, nltk, spacy, torchao>=0.17, and prettytable; services/jupyterhub/build/Dockerfile still downloads en_core_web_sm and vader_lexicon.
  • Pass 29 pre-fix verifier: python scripts/verify_repo.py --check all --fast reported 0 findings before the genai-vanilla bump was applied.
  • Pass 29 pre-fix affected suite: pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed (105 passed) before the mixed-closing-line regression was added.
  • Pass 29 red/green rewrite regressions: pytest tests/test_rewrite_imports.py::test_parenthesized_mixed_closing_line_drops_only_deprecated_params tests/test_rewrite_imports.py::test_parenthesized_mixed_closing_line_keeps_symbol_after_params -q failed before parenthesized import member lines were split into comma-separated symbols, then passed after the fix.
  • Pass 29 affected verifier/rewrite suite: pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed (107 passed).
  • Pass 29 final verifier: python scripts/verify_repo.py --check all --fast reported 0 findings after staging the vendor/genai-vanilla gitlink at c2ffe8d.
  • Pass 29 final validation: ruff check . --no-cache, make docs-build, python -m py_compile scripts/verify_repo.py scripts/rewrite_imports.py scripts/inject_smoke_test_cell.py scripts/edit_notebook_markdown.py, git diff --cached --check, and git diff --check passed.
  • Pass 29 full pytest: pytest tests/ -v passed (431 passed, 3 skipped, 17 warnings).
  • Pass 29 artifact validation: notebook JSON parse covered 51 notebooks; YAML parse covered .github/workflows/ci.yml, .github/workflows/pages.yml, scripts/verify_repo_config.yaml, mkdocs.yml, deploy/genai-vanilla-jupyterhub.override.yml, and vendor/genai-vanilla/services/jupyterhub/compose.yml; shellcheck/syntax passed for local and consumed vendor shell entrypoints.
  • Pass 29 audit validation: pip-audit -r docs-requirements.txt found no known vulnerabilities; pip-audit -r requirements.txt -r torch-requirements.txt still reported the ledgered 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • Pass 30 branch/upstream parity: git status --short --branch was clean at pass start, and git rev-list --left-right --count @{u}...HEAD returned 0 0.
  • Pass 30 genai-vanilla upstream check: upstream main advanced from c2ffe8d10f5f21c549b411d87861c83e518073ba to 10f840252404eb5399550f96fbb560153f1a47c7; git -C vendor/genai-vanilla diff --name-status c2ffe8d10f5f21c549b411d87861c83e518073ba..10f840252404eb5399550f96fbb560153f1a47c7 showed Perplexica/Vane research docs and a bootstrapper deferral test only.
  • Pass 30 JupyterHub runtime contract check: at 10f8402, the upstream delta did not touch consumed JupyterHub runtime files; current runtime docs and the dependency ledger were updated to 10f840252404eb5399550f96fbb560153f1a47c7.
  • Pass 30 pre-fix verifier: python scripts/verify_repo.py --check all --fast reported 0 findings before the genai-vanilla bump was applied.
  • Pass 30 pre-fix affected suite: pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed (107 passed) before the duplicate-import regression was added.
  • Pass 30 red/green rewrite regression: pytest tests/test_rewrite_imports.py::test_same_line_closing_parenthesized_nnparams_import_prevents_duplicate_injection -q failed before existing parenthesized NNParams imports with same-line closing parens were counted, then passed after the fix.
  • Pass 30 affected verifier/rewrite suite: pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed (108 passed).
  • Pass 30 final verifier: python scripts/verify_repo.py --check all --fast reported 0 findings after staging the vendor/genai-vanilla gitlink at 10f8402.
  • Pass 30 final validation: ruff check . --no-cache, make docs-build, python -m py_compile scripts/verify_repo.py scripts/rewrite_imports.py scripts/inject_smoke_test_cell.py scripts/edit_notebook_markdown.py, git diff --cached --check, and git diff --check passed.
  • Pass 30 full pytest: pytest tests/ -v passed (432 passed, 3 skipped, 17 warnings).
  • Pass 30 artifact validation: notebook JSON parse covered 51 notebooks; YAML parse covered .github/workflows/ci.yml, .github/workflows/pages.yml, scripts/verify_repo_config.yaml, mkdocs.yml, deploy/genai-vanilla-jupyterhub.override.yml, and vendor/genai-vanilla/services/jupyterhub/compose.yml; shellcheck/syntax passed for local and consumed vendor shell entrypoints.
  • Pass 30 audit validation: pip-audit -r docs-requirements.txt found no known vulnerabilities; pip-audit -r requirements.txt -r torch-requirements.txt still reported the ledgered 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • Pass 31 branch/upstream and submodule parity: git status --short --branch was clean, git rev-list --left-right --count @{u}...HEAD returned 0 0, and both git ls-remote https://github.com/thekaveh/genai-vanilla.git refs/heads/main and git submodule status vendor/genai-vanilla resolved to 10f840252404eb5399550f96fbb560153f1a47c7.
  • Pass 31 verifier: python scripts/verify_repo.py --check all --fast reported 0 findings before fixes.
  • Pass 31 pre-fix affected suite: pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed (108 passed) before the opener-line regression was added.
  • Pass 31 red/green rewrite regression: pytest tests/test_rewrite_imports.py::test_parenthesized_opener_line_members_are_rewritten -q failed before parenthesized import opener-line members were rewritten, then passed after the fix.
  • Pass 31 affected verifier/rewrite suite: pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed (109 passed).
  • Pass 31 final verifier: python scripts/verify_repo.py --check all --fast reported 0 findings after the rewrite-import fix.
  • Pass 31 final validation: ruff check . --no-cache, make docs-build, python -m py_compile scripts/verify_repo.py scripts/rewrite_imports.py scripts/inject_smoke_test_cell.py scripts/edit_notebook_markdown.py, git diff --cached --check, and git diff --check passed.
  • Pass 31 full pytest: pytest tests/ -v passed (433 passed, 3 skipped, 17 warnings).
  • Pass 31 artifact validation: notebook JSON parse covered 51 notebooks; YAML parse covered .github/workflows/ci.yml, .github/workflows/pages.yml, scripts/verify_repo_config.yaml, mkdocs.yml, deploy/genai-vanilla-jupyterhub.override.yml, and vendor/genai-vanilla/services/jupyterhub/compose.yml; shellcheck/syntax passed for local and consumed vendor shell entrypoints.
  • Pass 31 audit validation: pip-audit -r docs-requirements.txt found no known vulnerabilities; pip-audit -r requirements.txt -r torch-requirements.txt still reported the ledgered 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • Pass 32 branch/upstream and submodule parity: git status --short --branch was clean, git rev-list --left-right --count @{u}...HEAD returned 0 0, git submodule status vendor/genai-vanilla resolved to 10f840252404eb5399550f96fbb560153f1a47c7, and git ls-remote https://github.com/thekaveh/genai-vanilla.git refs/heads/main matched the same SHA.
  • Pass 32 verifier: python scripts/verify_repo.py --check all --fast reported 0 findings before fixes.
  • Pass 32 reviewer evidence: docs/published-surface reviewer found no new actionable docs issues; notebook reviewer found task-local ignored ./runs artifact policy ambiguity; tooling reviewer found workflow action-pin policy lacked verifier enforcement; Python reviewer found four rewrite/S2/CLI edge cases.
  • Pass 32 red/green rewrite regressions: pytest tests/test_rewrite_imports.py::test_qualified_and_declaration_param_names_are_not_rewritten tests/test_rewrite_imports.py::test_parenthesized_non_deprecated_import_preserves_comments tests/test_rewrite_imports.py::test_missing_input_path_returns_nonzero -q failed before the fixes, then passed after call-site context checks, raw no-op parenthesized-import preservation, and non-zero missing-path exits.
  • Pass 32 red/green verifier regressions: pytest tests/test_verify_repo.py::test_structure_s2_checks_missing_dotted_submodules tests/test_verify_repo.py::test_docs_d10_flags_workflow_action_refs_that_are_not_sha_pinned tests/test_verify_repo.py::test_docs_d10_flags_workflow_action_refs_missing_from_ledger tests/test_verify_repo.py::test_docs_d10_current_workflow_action_pins_match_ledger -q failed on the three new missing-behavior cases before fixes, then passed after full dotted import checking and D10 workflow action-pin validation.
  • Pass 32 affected verifier/rewrite suite: pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed (116 passed).
  • Pass 32 final verifier: python scripts/verify_repo.py --check all --fast reported 0 findings after fixes.
  • Pass 32 final validation: ruff check . --no-cache, make docs-build, python -m py_compile scripts/verify_repo.py scripts/rewrite_imports.py scripts/inject_smoke_test_cell.py scripts/edit_notebook_markdown.py, and git diff --check passed.
  • Pass 32 full pytest: pytest tests/ -v passed (440 passed, 3 skipped, 17 warnings).
  • Pass 32 artifact validation: notebook JSON parse covered 51 notebooks; YAML parse covered .github/workflows/ci.yml, .github/workflows/pages.yml, scripts/verify_repo_config.yaml, mkdocs.yml, deploy/genai-vanilla-jupyterhub.override.yml, and vendor/genai-vanilla/services/jupyterhub/compose.yml; shellcheck/syntax passed for local and consumed vendor shell entrypoints.
  • Pass 32 audit validation: pip-audit -r docs-requirements.txt found no known vulnerabilities; pip-audit -r requirements.txt -r torch-requirements.txt still reported the ledgered 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • Pass 33 branch/upstream and submodule parity: git status --short --branch was clean, git rev-list --left-right --count @{u}...HEAD returned 0 0, git submodule status vendor/genai-vanilla resolved to 10f840252404eb5399550f96fbb560153f1a47c7, and git ls-remote https://github.com/thekaveh/genai-vanilla.git refs/heads/main matched the same SHA.
  • Pass 33 verifier: python scripts/verify_repo.py --check all --fast reported 0 findings before fixes.
  • Pass 33 reviewer evidence: docs reviewer and notebook reviewer found no new actionable issues; tooling and Python reviewers independently found .yaml workflow action-pin bypass; Python reviewer also found deprecated Params import migration left non-call references stale.
  • Pass 33 red/green rewrite regression: pytest tests/test_rewrite_imports.py::test_non_call_param_references_are_rewritten_with_import -q failed before non-call deprecated Params references were rewritten, then passed after the token replacement broadened to unqualified executable references while preserving qualified attributes and declaration names.
  • Pass 33 red/green workflow regression: pytest tests/test_verify_repo.py::test_docs_d10_flags_yaml_workflow_action_refs_that_are_not_sha_pinned -q failed before .yaml workflows were scanned, then passed after D10 scanned both .yml and .yaml.
  • Pass 33 affected verifier/rewrite suite: pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed (118 passed).
  • Pass 33 final verifier: python scripts/verify_repo.py --check all --fast reported 0 findings after fixes.
  • Pass 33 final validation: ruff check . --no-cache, make docs-build, python -m py_compile scripts/verify_repo.py scripts/rewrite_imports.py scripts/inject_smoke_test_cell.py scripts/edit_notebook_markdown.py, and git diff --check passed.
  • Pass 33 full pytest: pytest tests/ -v passed (442 passed, 3 skipped, 17 warnings).
  • Pass 33 artifact validation: notebook JSON parse covered 51 notebooks; YAML parse covered .github/workflows/ci.yml, .github/workflows/pages.yml, scripts/verify_repo_config.yaml, mkdocs.yml, deploy/genai-vanilla-jupyterhub.override.yml, and vendor/genai-vanilla/services/jupyterhub/compose.yml; shellcheck/syntax passed for local and consumed vendor shell entrypoints.
  • Pass 33 audit validation: pip-audit -r docs-requirements.txt found no known vulnerabilities; pip-audit -r requirements.txt -r torch-requirements.txt still reported the ledgered 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • Pass 34 branch/upstream and submodule parity: git status --short --branch was clean, git rev-list --left-right --count @{u}...HEAD returned 0 0, git submodule status vendor/genai-vanilla resolved to 10f840252404eb5399550f96fbb560153f1a47c7, and git ls-remote https://github.com/thekaveh/genai-vanilla.git refs/heads/main matched the same SHA.
  • Pass 34 verifier and focused tests: python scripts/verify_repo.py --check all --fast reported 0 findings, and pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed (118 passed).
  • Pass 34 reviewer evidence: notebook/runtime, docs/published-surface, and Python verifier/rewrite reviewers found no new actionable issues; tooling/build reviewer found the genai-vanilla compose-config checklist omitted the required env file.
  • Pass 34 compose-config validation: ML_REPO_PATH="$PWD" ML_SSH_MOUNT_DIR="$HOME/.ssh" docker compose -f vendor/genai-vanilla/docker-compose.yml -f deploy/genai-vanilla-jupyterhub.override.yml config failed with missing environment variables and invalid blank image/build context; adding --env-file vendor/genai-vanilla/.env.example passed.
  • Pass 34 final validation: ruff check . --no-cache, make docs-build, python -m compileall scripts tests notebooks -q, git diff --check, notebook JSON parse (51), YAML parse, shellcheck/syntax checks, and full pytest (442 passed, 3 skipped, 17 warnings) passed.
  • Pass 34 audit validation: pip-audit -r docs-requirements.txt found no known vulnerabilities; pip-audit -r requirements.txt -r torch-requirements.txt still reported the ledgered 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • Pass 35 branch/upstream and submodule parity: git status --short --branch was clean, git rev-list --left-right --count @{u}...HEAD returned 0 0, git submodule status vendor/genai-vanilla resolved to 10f840252404eb5399550f96fbb560153f1a47c7, and git ls-remote https://github.com/thekaveh/genai-vanilla.git refs/heads/main matched the same SHA.
  • Pass 35 verifier and baseline validation: python scripts/verify_repo.py --check all --fast reported 0 findings, pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed before fixes (118 passed), and pre-fix pytest tests/ -v passed (442 passed, 3 skipped, 17 warnings).
  • Pass 35 reviewer evidence: notebook/runtime, docs/published-surface, and tooling/build reviewers found no new actionable issues; Python reviewer found two rewrite-import preservation regressions involving no-op single-line parenthesized imports and comments inside changed parenthesized imports.
  • Pass 35 red/green rewrite regressions: pytest tests/test_rewrite_imports.py::test_single_line_parenthesized_non_deprecated_import_is_preserved tests/test_rewrite_imports.py::test_parenthesized_rewrite_preserves_kept_member_comments -q failed before the fix, then passed after conditional single-line normalization and member-line comment preservation.
  • Pass 35 affected rewrite/verifier suites: pytest tests/test_rewrite_imports.py -q passed (31 passed), pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed (120 passed), and python scripts/verify_repo.py --check all --fast reported 0 findings after fixes.
  • Pass 35 artifact/tooling validation: ruff check . --no-cache, make docs-build, python -m compileall scripts tests notebooks -q, git diff --check, notebook JSON parse (51), YAML parse, shellcheck/syntax checks, and compose-config validation with vendor/genai-vanilla/.env.example passed.
  • Pass 35 full pytest after fixes: pytest tests/ -v passed (444 passed, 3 skipped, 17 warnings).
  • Pass 35 audit validation: pip-audit -r docs-requirements.txt found no known vulnerabilities; pip-audit -r requirements.txt -r torch-requirements.txt still reported the ledgered 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • Pass 36 branch/upstream and submodule parity: git status --short --branch was clean, git rev-list --left-right --count @{u}...HEAD returned 0 0, git submodule status vendor/genai-vanilla resolved to 10f840252404eb5399550f96fbb560153f1a47c7, and git ls-remote https://github.com/thekaveh/genai-vanilla.git refs/heads/main matched the same SHA.
  • Pass 36 verifier and baseline validation: python scripts/verify_repo.py --check all --fast reported 0 findings, pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed before fixes (120 passed), and pre-fix pytest tests/ -v passed (444 passed, 3 skipped, 17 warnings).
  • Pass 36 reviewer evidence: notebook/runtime, docs/published-surface, and tooling/build reviewers found no new actionable issues; Python reviewer found that comma-separated common imports such as import os, common.utils bypassed both S5 verification and notebook import rewriting.
  • Pass 36 red/green import-alias regressions: pytest tests/test_rewrite_imports.py::test_module_path_rewrite_common_alias_inside_multi_import tests/test_verify_repo.py::test_structure_s5_flags_common_alias_inside_python_multi_import tests/test_verify_repo.py::test_structure_s5_flags_common_alias_inside_notebook_multi_import -q failed before the fix, then passed (3 passed) after S5 switched to AST-backed import alias extraction and rewrite_imports.py rewrote common aliases inside import lists.
  • Pass 36 affected rewrite/verifier suites: pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed (123 passed), and python scripts/verify_repo.py --check all --fast reported 0 findings after fixes.
  • Pass 36 artifact/tooling validation: ruff check . --no-cache, make docs-build, python -m compileall scripts tests notebooks -q, git diff --check, notebook JSON parse (51), YAML parse, shellcheck/syntax checks, and compose-config validation with vendor/genai-vanilla/.env.example passed.
  • Pass 36 full pytest after fixes: pytest tests/ -v passed (447 passed, 3 skipped, 17 warnings).
  • Pass 36 audit validation: pip-audit -r docs-requirements.txt found no known vulnerabilities; pip-audit -r requirements.txt -r torch-requirements.txt still reported the ledgered 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • Pass 37 branch/upstream and submodule parity: git status --short --branch was clean, git rev-list --left-right --count @{u}...HEAD returned 0 0, git submodule status vendor/genai-vanilla resolved to 10f840252404eb5399550f96fbb560153f1a47c7, and git ls-remote https://github.com/thekaveh/genai-vanilla.git refs/heads/main matched the same SHA.
  • Pass 37 verifier and baseline validation: python scripts/verify_repo.py --check all --fast reported 0 findings before fixes, pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed before fixes (123 passed), and lint/docs/compile/diff checks passed before fixes.
  • Pass 37 reviewer evidence: tooling/build reviewer found no new actionable issues; docs reviewer found historical issue-count drift in pass-history accounting; notebook/runtime and Python reviewers found rewrite-import mutation of non-Python text and Python reviewer found additional alias, fallback, and closing-comment edge cases.
  • Pass 37 red/green regressions: pytest tests/test_rewrite_imports.py::test_module_path_rewrite_preserves_multiline_strings tests/test_rewrite_imports.py::test_module_path_rewrite_skips_non_python_cell_magic tests/test_rewrite_imports.py::test_existing_aliased_nnparams_import_suppresses_identical_injection tests/test_rewrite_imports.py::test_parenthesized_rewrite_preserves_closing_paren_comment tests/test_verify_repo.py::test_structure_s2_fallback_ignores_parentheses_in_import_comments -q failed before the fixes, then passed (5 passed) after protecting multiline strings and non-Python cell magics, comparing canonical NNParams import requirements, preserving closing comments, and making fallback parenthesis balance token-aware.
  • Pass 37 affected rewrite/verifier suite: pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed (128 passed), and python scripts/verify_repo.py --check all --fast reported 0 findings after fixes.
  • Pass 37 artifact/tooling validation: ruff check . --no-cache, make docs-build, python -m compileall scripts tests notebooks -q, git diff --check, notebook JSON parse (51), YAML parse, shellcheck/syntax checks, compose-config validation with vendor/genai-vanilla/.env.example, and maintenance-log chronology/issue reconciliation passed.
  • Pass 37 full pytest after fixes: pytest tests/ -v passed (452 passed, 3 skipped, 17 warnings).
  • Pass 37 audit validation: pip-audit -r docs-requirements.txt found no known vulnerabilities; pip-audit -r requirements.txt -r torch-requirements.txt still reported the ledgered 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • Pass 38 branch/upstream and submodule parity: git status --short --branch was clean, git rev-list --left-right --count @{u}...HEAD returned 0 0, git submodule status vendor/genai-vanilla resolved to 10f840252404eb5399550f96fbb560153f1a47c7, and git ls-remote https://github.com/thekaveh/genai-vanilla.git refs/heads/main matched the same SHA.
  • Pass 38 verifier and baseline validation: python scripts/verify_repo.py --check all --fast reported 0 findings before fixes, pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed before fixes (128 passed), and lint/docs/compile/diff checks passed before fixes.
  • Pass 38 reviewer evidence: docs/published-surfaces and tooling/build reviewers found no new actionable issues; Python reviewer found local binding-position rewrites and from common import utils migration coverage gaps; notebook/runtime reviewer found eight active Reddit notebooks with cell IDs but nbformat_minor: 2, plus the S1 verifier schema-validation blind spot.
  • Pass 38 red/green regressions: pytest tests/test_rewrite_imports.py::test_module_path_rewrite_from_common_import_utils tests/test_rewrite_imports.py::test_param_name_references_preserve_binding_positions tests/test_verify_repo.py::test_structure_s1_flags_invalid_notebook_schema -q failed before the fixes, then passed (3 passed) after adding the import mapping, protecting deprecated-name local bindings, and schema-validating raw notebooks.
  • Pass 38 notebook schema repair: nbformat.validate failed before the metadata repair for eight active Reddit phase2/phase3 notebooks with cell IDs and nbformat_minor: 2, then all 51 notebooks schema-validated after updating those notebooks to nbformat_minor: 5.
  • Pass 38 affected rewrite/verifier suite: pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed (131 passed), and python scripts/verify_repo.py --check all --fast reported 0 findings after fixes.
  • Pass 38 artifact/tooling validation: ruff check . --no-cache, make docs-build, python -m compileall scripts tests notebooks -q, git diff --check, notebook schema validation (51), YAML parse, shellcheck/syntax checks, compose-config validation with vendor/genai-vanilla/.env.example, and maintenance-log chronology/issue reconciliation passed.
  • Pass 38 full pytest after fixes: pytest tests/ -v passed (455 passed, 3 skipped, 17 warnings).
  • Pass 38 audit validation: pip-audit -r docs-requirements.txt found no known vulnerabilities; pip-audit -r requirements.txt -r torch-requirements.txt still reported the ledgered 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • Pass 39 branch/upstream and baseline validation: git status --short --branch was clean, git rev-list --left-right --count @{u}...HEAD returned 0 0, python scripts/verify_repo.py --check all --fast reported 0 findings before fixes, and pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed before fixes (131 passed).
  • Pass 39 reviewer evidence: docs/published-surfaces and tooling/build reviewers found no new actionable issues; Python reviewer found that the pass-38 cell-wide deprecated Params binding protection could leave stale imported GraphAttNNParams reads when a later local binding reused the same name; notebook/runtime reviewer found that S1 raw schema validation skipped archive notebooks and all 22 archived CodeXGLUE notebooks lacked raw cell.id fields.
  • Pass 39 red/green regressions: pytest tests/test_rewrite_imports.py::test_imported_param_name_reads_rewrite_even_with_later_local_binding -q failed before the fix, then passed after deprecated Params local-binding protection became token-position-aware; pytest tests/test_verify_repo.py::test_structure_s1_flags_missing_archive_notebook_cell_id -q failed before the fix, then passed after S1 gained a dedicated all-notebook raw schema iterator.
  • Pass 39 archive notebook schema repair: the 22 archived CodeXGLUE notebooks promoted existing metadata.id values to raw nbformat cell.id fields and updated nbformat_minor to 5; an independent nbformat.validate sweep confirmed all 51 notebooks now schema-validate and have cell IDs.
  • Pass 39 affected rewrite/verifier suite: pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed (133 passed), python scripts/verify_repo.py --check structure --fast reported 0 findings, and python scripts/verify_repo.py --check all --fast reported 0 findings after fixes.
  • Pass 39 artifact/tooling validation: ruff check . --no-cache, make docs-build, python -m compileall scripts tests notebooks -q, git diff --check, notebook schema validation (51), YAML parse, shellcheck/syntax checks, compose-config validation with vendor/genai-vanilla/.env.example, and maintenance-log chronology/issue reconciliation passed.
  • Pass 39 full pytest after fixes: pytest tests/ -v passed (457 passed, 3 skipped, 17 warnings).
  • Pass 39 audit validation: pip-audit -r docs-requirements.txt found no known vulnerabilities; pip-audit -r requirements.txt -r torch-requirements.txt still reported the ledgered 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • Pass 40 branch/upstream and baseline validation: git status --short --branch was clean, git rev-list --left-right --count @{u}...HEAD returned 0 0, python scripts/verify_repo.py --check all --fast reported 0 findings, and pre-fix focused rewrite/verifier tests passed (133 passed).
  • Pass 40 reviewer evidence: notebook/runtime and tooling/build reviewers found no new actionable issues; docs reviewer found published page numbering drift in docs/index.md and docs/architecture.md plus D9 coverage gaps for those pages; Python reviewer found that continuation call-site rewriting used original protected token positions after import lines were dropped, so continued local bindings could be renamed incorrectly.
  • Pass 40 red/green regressions: pytest tests/test_rewrite_imports.py::test_continued_local_binding_stays_protected_after_import_drop -q failed before the fix and passed after recomputing binding protection from the post-import-rewrite line set; pytest tests/test_verify_repo.py::test_docs_d9_flags_malformed_published_docs_page_heading -q failed before the fix and passed after D9 included published MkDocs pages.
  • Pass 40 affected rewrite/verifier suite: pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed (135 passed), python scripts/verify_repo.py --check docs --fast reported 0 findings, and python scripts/verify_repo.py --check all --fast reported 0 findings after fixes.
  • Pass 40 artifact/tooling validation: ruff check . --no-cache, make docs-build, python -m compileall scripts tests notebooks -q, git diff --check, notebook schema validation (51), YAML parse, shellcheck/syntax checks, compose-config validation with vendor/genai-vanilla/.env.example, and maintenance-log chronology/issue reconciliation passed.
  • Pass 40 full pytest after fixes: pytest tests/ -v passed (459 passed, 3 skipped, 17 warnings).
  • Pass 40 audit validation: pip-audit -r docs-requirements.txt found no known vulnerabilities; pip-audit -r requirements.txt -r torch-requirements.txt still reported the ledgered 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • Pass 41 branch/upstream and baseline validation: git status --short --branch was clean, git rev-list --left-right --count @{u}...HEAD returned 0 0, python scripts/verify_repo.py --check all --fast reported 0 findings, and pre-fix focused rewrite/verifier tests passed (135 passed).
  • Pass 41 reviewer evidence: notebook/runtime, docs/published-surfaces, and tooling/build reviewers found no new actionable issues; Python reviewer found class/function definition names were not treated as local bindings during deprecated Params rewrites and D9 still missed the published diagram provenance page.
  • Pass 41 red/green regressions: pytest tests/test_rewrite_imports.py::test_local_class_and_function_bindings_stay_protected_after_import_drop -q failed before the fix and passed after class/function definitions became local binding positions; pytest tests/test_verify_repo.py::test_docs_d9_flags_malformed_published_diagram_provenance_heading -q failed before the fix and passed after D9 included docs/diagrams/README.md.
  • Pass 41 affected rewrite/verifier suite: pytest tests/test_rewrite_imports.py tests/test_verify_repo.py -q passed (137 passed), python scripts/verify_repo.py --check docs --fast reported 0 findings, and python scripts/verify_repo.py --check all --fast reported 0 findings after fixes.
  • Pass 41 artifact/tooling validation: ruff check . --no-cache, make docs-build, python -m compileall scripts tests notebooks -q, git diff --check, notebook schema validation (51), YAML parse, shellcheck/syntax checks, compose-config validation with vendor/genai-vanilla/.env.example, and maintenance-log chronology/issue reconciliation passed.
  • Pass 41 full pytest after fixes: pytest tests/ -v passed (461 passed, 3 skipped, 17 warnings).
  • Pass 41 audit validation: pip-audit -r docs-requirements.txt found no known vulnerabilities; pip-audit -r requirements.txt -r torch-requirements.txt still reported the ledgered 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • Pass 42 branch/upstream and baseline validation: git status --short --branch was clean, git rev-list --left-right --count @{u}...HEAD returned 0 0, python scripts/verify_repo.py --check all --fast reported 0 findings, and pre-fix focused rewrite/verifier tests passed (137 passed).
  • Pass 42 reviewer evidence: docs/published-surfaces reviewer found no new actionable issues; Python reviewer found function-scope binding protection still used module-style position semantics; notebook/runtime reviewer found stale cross-language archive outputs for notebooks whose model/ text artifacts are not tracked; tooling reviewer found setup targets ignored PYTHON=... for pip and NLP asset commands.
  • Pass 42 red/green regressions: pytest tests/test_rewrite_imports.py::test_function_local_read_before_assignment_stays_protected_after_import_drop -q failed before the fix and passed after function/lambda/comprehension scopes protected all same-scope deprecated-name references; pytest tests/nnx_surface/test_notebook_api_surface.py::test_archive_cross_language_missing_model_outputs_match_tracked_artifacts -q failed before refreshing the eight missing-artifact archive outputs and passed after the outputs used relative guard paths; pytest tests/test_makefile_contract.py::test_setup_targets_use_selected_python_interpreter -q failed before setup commands routed through $(PYTHON)/$(PIP) and passed after.
  • Pass 42 affected suites: pytest tests/test_rewrite_imports.py tests/nnx_surface/test_notebook_api_surface.py tests/test_makefile_contract.py -q passed (341 passed, 3 warnings), python scripts/verify_repo.py --check all --fast reported 0 findings, and all 51 notebooks schema-validated with nbformat.validate.
  • Pass 42 artifact/tooling validation: ruff check . --no-cache, make docs-build, python -m compileall scripts tests notebooks -q, git diff --check, YAML parse, shellcheck/syntax checks for local and consumed JupyterHub entrypoints, compose-config validation with wrapper-equivalent ML_REPO_PATH/ML_SSH_MOUNT_DIR plus vendor/genai-vanilla/.env.example, and maintenance-log chronology/issue reconciliation passed.
  • Pass 42 full pytest after fixes: pytest tests/ -v passed (464 passed, 3 skipped, 17 warnings).
  • Pass 42 audit validation: pip-audit -r docs-requirements.txt found no known vulnerabilities; pip-audit -r requirements.txt -r torch-requirements.txt still reported the ledgered 23 known vulnerabilities in torch, pytorch-lightning, and nltk.
  • Pass 43 branch/upstream and baseline validation: git status --short --branch was clean, git rev-list --left-right --count @{u}...HEAD returned 0 0, python scripts/verify_repo.py --check all --fast reported 0 findings, and the focused pass-42 regression suites passed (341 passed, 3 warnings).
  • Pass 43 full validation: pytest -q passed (464 passed, 3 skipped, 17 warnings), ruff check . --no-cache passed, make docs-build passed with the known upstream Material for MkDocs 2.0 warning, python -m compileall scripts tests notebooks -q passed, git diff --check passed, and notebook JSON parse covered all 51 tracked notebooks.
  • Pass 43 naming sweep: rg found only the documented/deferred genai-vanilla stale-comment limitation, historical maintenance-log mentions, verifier patterns for detecting stale names, and archive model text content; no new actionable ml-lab references were counted.
  • Pass 44 branch/upstream and consumed-contract validation: git status --short --branch was clean, branch/upstream parity returned 0 0, git submodule status vendor/genai-vanilla and git ls-remote https://github.com/thekaveh/genai-vanilla.git refs/heads/main both resolved to 10f840252404eb5399550f96fbb560153f1a47c7, and python scripts/verify_repo.py --check all --fast reported 0 findings.
  • Pass 44 docs/notebook/static validation: a local Markdown-link checker scanned 28 Markdown files with 0 missing local links; published numbered-heading probe reported 0 issues; notebook source hazard scan found 0 stale repo-path/CWD/data/runs hazards; YAML parse covered workflows, MkDocs, verifier config, and the JupyterHub override; all 51 notebooks parsed as JSON.
  • Pass 44 execution/tooling validation: focused rewrite/verifier/notebook/Makefile suite passed (437 passed, 3 warnings); ruff check . --no-cache, make docs-build, python -m compileall scripts tests notebooks -q, git diff --check, shellcheck/syntax for local and consumed vendor entrypoints, compose config, and pip-audit -r docs-requirements.txt passed; pip-audit -r requirements.txt -r torch-requirements.txt still reported the ledgered 23 accepted findings.
  • Pass 44 full pytest: pytest -q passed (464 passed, 3 skipped, 17 warnings).
  • Pass 45 branch/verifier validation: git status --short --branch was clean, branch/upstream parity returned 0 0, and python scripts/verify_repo.py --check all --fast reported 0 findings.
  • Pass 45 notebook relocation/artifact validation: project notebook scan found 0 notebooks outside notebooks/ after excluding vendored service notebooks; all archive notebooks remain under notebooks/archive/; task-local data/runs structural probe found 0 issues; git ls-files 'notebooks/**/data/**' 'notebooks/**/runs/**' 'notebooks/**/__pycache__/**' returned no tracked artifacts; notebook source scan found 0 ../data, ../runs, or old os.path.abspath(os.curdir) hazards.
  • Pass 45 repo-name validation: stale ml-lab sweep outside excluded historical/vendor/dependency-ledger surfaces found only the verifier regex used to detect stale github.com/thekaveh/ml-lab URLs.
  • Pass 45 final validation: pytest -q passed (464 passed, 3 skipped, 17 warnings), ruff check . --no-cache, make docs-build, python -m compileall scripts tests notebooks -q, notebook JSON parse (51), YAML parse (5 files), git diff --check, and compose config passed.
  • Pass 46 branch/verifier/collection validation: git status --short --branch was clean, branch/upstream parity returned 0 0, python scripts/verify_repo.py --check all --fast reported 0 findings, and root python -m pytest --collect-only -q -p no:cacheprovider collected 467 intended tests without vendored collection errors.
  • Pass 46 Makefile/tooling validation: make -n check-tier-a-clean and make check-tier-a-clean both scoped to the configured Tier-A notebooks; ruff check . --no-cache, make docs-build, python -m compileall scripts tests notebooks -q, shellcheck/syntax for local and consumed vendor entrypoints, pip-audit -r docs-requirements.txt, and git diff --check passed.
  • Pass 46 full pytest: pytest -q passed (464 passed, 3 skipped, 17 warnings).
  • Pass 47 branch/verifier/docs validation: git status --short --branch was clean, branch/upstream parity returned 0 0, python scripts/verify_repo.py --check docs --fast and python scripts/verify_repo.py --check all --fast reported 0 findings, MkDocs nav had 13 targets with 0 missing files, and Markdown local-link scan covered 28 files with 0 missing local links.
  • Pass 47 published/current-runtime validation: published H2 numbering probe reported 0 issues; README/CONTRIBUTING/runtime docs/dependency ledger contained the current genai-vanilla pin 10f840252404eb5399550f96fbb560153f1a47c7 and thekaveh-nnx[lm]==0.2.0; older genai-vanilla SHA hits outside the maintenance log were limited to intentional dependency-ledger history.
  • Pass 47 final validation: make docs-build, ruff check . --no-cache, python -m compileall scripts tests notebooks -q, git diff --check, and pytest -q passed (464 passed, 3 skipped, 17 warnings).
  • Pass 48 branch/verifier validation: git status --short --branch was clean, branch/upstream parity returned 0 0, and both python scripts/verify_repo.py --check structure --fast and python scripts/verify_repo.py --check all --fast reported 0 findings.
  • Pass 48 Python tooling validation: focused pytest tests/test_rewrite_imports.py tests/test_verify_repo.py tests/test_edit_notebook_markdown.py tests/test_inject_smoke_test_cell.py tests/test_makefile_contract.py -q passed (148 passed); python -m py_compile covered verifier, rewrite, smoke-cell, and notebook-markdown helper scripts; direct migration-residue scan found expected old-name fixtures only in tests and rewrite-migration code; scripts/tests AST parsed; ruff check scripts tests --no-cache passed.
  • Pass 48 final validation: make docs-build, python -m compileall scripts tests notebooks -q, git diff --check, and pytest -q passed (464 passed, 3 skipped, 17 warnings).
  • Pass 49 branch/verifier/notebook validation: git status --short --branch was clean, branch/upstream parity returned 0 0, python scripts/verify_repo.py --check execution --fast and python scripts/verify_repo.py --check all --fast reported 0 findings, and focused notebook/runtime tests passed (302 passed, 3 skipped, 3 warnings).
  • Pass 49 notebook artifact validation: all 51 notebooks validated with nbformat.validate; direct JSON scans found 0 committed error outputs and 0 transient path leaks; archive shape probe found only notebooks/archive/codexglue_summarization/src without a notebook, which is the shared helper snapshot rather than an archive task directory.
  • Pass 49 final validation: ruff check . --no-cache, make docs-build, python -m compileall scripts tests notebooks -q, compose config, git diff --check, and pytest -q passed (464 passed, 3 skipped, 17 warnings).
  • Pass 50 branch/upstream/verifier validation: git status --short --branch was clean, branch/upstream parity returned 0 0, git submodule status vendor/genai-vanilla and git ls-remote https://github.com/thekaveh/genai-vanilla.git refs/heads/main both resolved to 10f840252404eb5399550f96fbb560153f1a47c7, and python scripts/verify_repo.py --check all --fast reported 0 findings.
  • Pass 50 capstone validation: all 51 notebooks validated with nbformat.validate; ruff check . --no-cache, make docs-build, python -m compileall scripts tests notebooks -q, git diff --check, shellcheck/syntax for local and consumed vendor entrypoints, pip-audit -r docs-requirements.txt, compose config, and pytest -q passed (464 passed, 3 skipped, 17 warnings).
  • Pass 50 audit/cap disposition: pip-audit -r requirements.txt -r torch-requirements.txt still reported the ledgered 23 accepted findings; pass 50 was a zero-issue pass, bringing the post-pass-42 streak to 8/20, and the maintenance loop stopped because MAX_PASSES=50 was reached.

4. Issue Log

ID Severity Category Location Description Status Validation
OM-001 Medium §3.6 docs / §3.8 documentation indexing docs/superpowers/*, docs/maintenance/*, README.md, mkdocs.yml The notebook-reorganization design and implementation records were tracked under ignored docs/superpowers/ paths and were not discoverable from README or the generated docs navigation. Fixed Moved the records to docs/maintenance/, indexed them in README and MkDocs nav, and validated docs/verifier/build paths.
OM-002 Low §3.9 numbered docs docs/maintenance/notebooks-reorganization-*.md The surfaced maintenance records used H2 headings such as 1.1. even though the current D9 verifier expects H2 headings to use one numeric component. Fixed Normalized their H1/H2 structure; python scripts/verify_repo.py --check docs --fast now reports 0 findings.
OM-003 Medium §3.8 link hygiene / §3.13 tests scripts/verify_repo.py, tests/test_verify_repo.py Markdown link and terminology sweeps only covered shallow docs/*.md, so nested maintenance docs could drift outside S3/D8 coverage. Fixed Added a red/green nested-doc broken-link regression and changed the in-scope docs iterator to include nested non-superpowers docs.
OM-004 Medium §3.23 error handling / §3.17 CLI trace scripts/verify_repo.py, tests/test_verify_repo.py Short external verifier subprocesses could run without bounded timeouts when callers omitted an explicit timeout. Fixed Added a default subprocess timeout, applied it to git ls-files, preserved long notebook-target overrides, and added regression coverage.
OM-005 Medium §3.17 notebook trace / §3.31 PyG contract scripts/verify_repo.py, tests/test_verify_repo.py The full-execution runtime canary checked only torch and torch_geometric, missing PyG extension modules required by graph notebooks. Fixed Expanded the canary to torch_sparse, torch_scatter, torch_cluster, torch_spline_conv, and pyg_lib; added a false-positive regression.
OM-006 High §3.31 consumed contracts / §3.13 tests tests/nnx_surface/test_notebook_api_surface.py, docs/dependency-contracts.md Local NNx surface tests can validate an editable sibling checkout instead of exact pinned thekaveh-nnx[lm]==0.2.0 without that nuance being recorded. Documented/deferred Ledger now records the PyPI pin as canonical, the editable override boundary, and the command to detect editable installs; enforcing failure for editable local dev is deferred to an explicit environment-policy change.
OM-007 Medium §3.31 consumed contracts / §3.17 runtime trace .gitmodules, vendor/genai-vanilla, scripts/start-jupyterhub.sh, deploy/genai-vanilla-jupyterhub.override.yml, docs/dependency-contracts.md The vendored genai-vanilla submodule contract and behind-upstream state were implicit instead of ledgered. Fixed/documented Added exact submodule pin, upstream SHA observed on 2026-07-04, wrapper/override expectations, and upgrade criteria to the dependency contract ledger.
OM-008 Medium §3.32 examples/library-fit Active notebooks using nnx.nn.*, nnx.utils, and nnx.vis_utils imports Several active examples still teach deep NNx module paths even when the top-level nnx facade exports the symbols. Deferred Migration requires a notebook source/output sweep and Tier-C baseline handling, so it remains a separate notebook modernization pass.
OM-009 Medium §3.32 examples/library-fit notebooks/diffusion-mnist-ddpm-pytorch/, notebooks/moe-fmnist-mixture-of-experts-pytorch/, notebooks/self_supervised-fmnist-jepa-pytorch/ Three notebooks still rebuild loaders manually from NNDataset internals instead of using NNDataset(batch_sizes=...). Deferred Needs notebook execution/output refresh to avoid stale committed outputs; keep grouped with the NNx facade-import modernization.
OM-010 Medium §3.17 notebook trace / §3.13 tests Active notebook outputs, scripts/verify_repo.py Stale-output detection is pre-positioned on optional metadata.source_hash, but current output-bearing cells have no hash marker, making the check a no-op today. Deferred Requires a notebook execution hook and one refresh cycle to stamp hashes before missing hashes can become warnings or errors.
OM-011 High §3.33 published docs surfaces GitHub Pages, default-branch README, repository About homepage The generated docs site is scaffolded and branch-local docs are current, but live Pages still returns 404 and the default-branch README/About surfaces remain behind this branch until the workflow and docs land on main. The live wiki is now a current signpost as of pass 6. Deferred Cannot complete from the maintenance branch without modifying default-branch live deployment state; keep README homepage as safer temporary metadata until Pages is live, then update About links.
OM-012 Low §3.14 CI/tooling .github/workflows/ci.yml, GitHub Actions branch runs Local validation is current, but GitHub Actions has no fresh branch CI run for this head. Deferred Trigger/open PR workflow after pushing this branch so GitHub validates the pushed commit.
OM-013 Medium §3.8 docs indexing / §3.33 published surfaces docs/index.md The generated-docs homepage still routed "Maintenance Log" readers to the July 2 hard-cap log instead of the active July 4 maintenance record. Fixed Updated the recommended reading path to name the current July 4 log and retain the July 2 log as historical context; docs verifier reports 0 findings.
OM-014 Medium §3.6 generated artifacts / §3.33 diagrams docs/diagrams/, docs/architecture.md, README.md, mkdocs.yml Checked-in diagram HTML artifacts had no provenance or regeneration contract in the docs navigation. Fixed Added docs/diagrams/README.md, linked it from architecture docs and README, and added it to MkDocs navigation.
OM-015 Low §3.8 documentation tone CHANGELOG.md A decorative checkmark glyph remained in a changelog entry, contradicting the repository's plain professional docs tone. Fixed Replaced the glyph with prose; git diff --check stays clean.
OM-016 Medium §3.29 supply-chain reproducibility .github/workflows/ci.yml, .github/workflows/pages.yml, docs/dependency-contracts.md Several GitHub Actions were exact-SHA pinned to older reviewed majors while newer stable major tags existed. Fixed Resolved current tag SHAs with git ls-remote --tags, updated workflow pins/comments, and ledgered the reviewed action tags and upgrade process.
OM-017 Medium §3.14 CI/tooling / §3.23 resilience .github/workflows/pages.yml Pages build and deploy jobs lacked explicit timeout-minutes, so hung doc deploys could consume the platform default. Fixed Added 15-minute build and 10-minute deploy caps; workflow YAML parses successfully.
OM-018 Medium §3.17 notebook execution / §3.23 resilience Makefile, docs/dependency-contracts.md Direct papermill targets had no --start-timeout or --execution-timeout bounds. Fixed Added centralized PAPERMILL_START_TIMEOUT and PAPERMILL_EXECUTION_TIMEOUT variables and passed them to Tier-A/B/C notebook targets; documented the CLI contract.
OM-019 Medium §3.29 build reproducibility Makefile, Dockerfile, docs/dependency-contracts.md Bootstrap paths still upgrade/install pip and setuptools without exact pins. Documented/deferred Added the bootstrap tooling gap to the dependency ledger; full pinning remains grouped with the lockfile/base-image digest pass because it changes every environment creation path.
OM-020 Low §3.32 examples/library-fit docs docs/FINDINGS-NNX.md The NNx findings doc overstated the NNDataset loader-bypass set by counting TinyShakespeare, which intentionally uses a custom sequence-window dataset. Fixed Updated the finding to distinguish the three NNDataset bypasses from the TinyShakespeare custom language-modeling dataset.
OM-021 High §3.4 correctness / §3.13 tests notebooks/image_classification-mnist-ffnn-numpy/linear_layer.py, tests/test_numpy_layers.py LinearLayer accepted supplied W/b arrays with incompatible shapes, then failed later or silently violated constructor dimensions. Fixed Added failing shape-regression tests first, then explicit constructor ValueError checks; focused tests now pass.
OM-022 Medium §3.30 code complexity scripts/verify_repo.py, scripts/rewrite_imports.py Maintenance scripts still exceed ideal complexity thresholds after the current pass. Deferred Refactoring is material and behavior-sensitive; keep it as a separate red/green script-maintainability pass rather than mixing it with workflow/docs/notebook-helper fixes.
OM-023 Low §3.10 dead code notebooks/image_classification-mnist-ffnn-numpy/consts.py, scripts/verify_repo.py Unused constants remained after the notebook reorganization and prior verifier refactors. Fixed Removed unused NumPy dataset-stat constants and stale verifier directory constants; focused verifier tests and py_compile pass.
OM-024 Medium §3.17 notebook trace / §3.13 tests Active notebook metadata.papermill, scripts/verify_repo.py, tests/test_verify_repo.py Seventeen committed active notebooks retained top-level metadata.papermill.output_path values under /tmp/*_out.ipynb, making source notebooks look like smoke-output artifacts. Fixed Added a failing E14 verifier regression, implemented E14.tmp_papermill_output_path, stripped the stale top-level papermill metadata, and reran python scripts/verify_repo.py --check execution --fast to 0 findings.
OM-025 Low §3.32 examples/library-fit docs notebooks/self_supervised-fmnist-jepa-pytorch/README.md, notebooks/moe-fmnist-mixture-of-experts-pytorch/README.md Two README files still described the TinyShakespeare transformer notebook as part of the NNDataset default-batch workaround, despite its custom sequence dataset. Fixed Updated the wording to refer only to the diffusion, MoE, and JEPA NNDataset workaround set.
OM-026 Medium §3.31 consumed contracts docs/dependency-contracts.md, vendor/genai-vanilla The genai-vanilla ledger's observed upstream main SHA was stale after a new upstream commit; the JupyterHub service wording also implied the top-level compose file defined the service directly rather than including its fragment. Fixed Updated the observed upstream SHA to b0bce0fc4e9d2bb282fbc6c97631f3e37233e24e; verified pinned c89eb5e7... has start.sh, top-level docker-compose.yml, and services/jupyterhub/compose.yml defining jupyterhub.
OM-027 Low §3.31 consumed contracts scripts/start-jupyterhub.sh, deploy/genai-vanilla-jupyterhub.override.yml Wrapper comments said vendor/genai-vanilla was "pinned to main" even though the repository uses a pinned submodule snapshot that can intentionally lag upstream main. Fixed Reworded the wrapper and override comments to describe a pinned submodule snapshot; shellcheck and bash syntax validation cover the wrapper.
OM-028 Low §3.29 build reproducibility / §3.31 consumed contracts docs/dependency-contracts.md, Dockerfile The bootstrap tooling ledger said the Dockerfile installed pip setuptools wheel, but the Dockerfile currently upgrades only pip and setuptools. Fixed Corrected the ledger wording and kept the broader exact-pin hardening under OM-019.
OM-029 Medium §3.17 notebook execution / §3.32 examples-library fit notebooks/node_classification-reddit-gnn-pyg/phase2-model-selection-notebook4.ipynb, tests/nnx_surface/test_notebook_api_surface.py The extended GAT notebook trained a single local runs list but ranked NNRun.all(), so committed "best run" outputs could show a cross-experiment graph_sage run instead of the notebook's GAT run. Fixed Added a failing static guard, changed the notebook to rank local runs, updated the markdown, cleared stale dependent outputs, and reran the focused guard plus notebook JSON parse.
OM-030 Medium §3.13 tests / §3.32 examples-library fit tests/nnx_surface/test_quantization_mnist_ffnn_pytorch.py, notebooks/quantization-mnist-ffnn-pytorch/ The manual-only quantization notebook depended on nnx.quantize_int8, nnx.qat_train_step_factory, and nnx.QATLifecycleCallback, but no fast CI/surface guard covered those facade contracts after the notebook left papermill tiers. Fixed Added quantization facade signature checks plus backend-gated PTQ/QAT smoke tests that skip cleanly when torchao or torch.int1 is unavailable; focused tests pass.
OM-031 Low §3.31 consumed contracts docs/dependency-contracts.md, vendor/genai-vanilla The genai-vanilla ledger's observed upstream main SHA drifted again from b0bce0fc... to 0e4e9643...; at pass 5 the superproject gitlink still pinned c89eb5e7.... Fixed Updated the observed upstream SHA to 0e4e9643ac273c6f36f815a5f4b3b187876bac74; pass 6 later consumed that upstream SHA through OM-033.
OM-032 Low §3.17 notebook execution / §3.13 tests scripts/verify_repo.py, tests/test_verify_repo.py, four active source notebooks Four active source notebooks still carried top-level metadata.papermill with source-notebook output paths, so they looked partly like generated papermill outputs even after /tmp paths were removed. Fixed Added a failing E14 regression, broadened E14 to flag any active source-notebook top-level papermill metadata, removed the stale metadata blocks, and reran the execution verifier to 0 findings.
OM-033 High §3.31 consumed contracts / §3.17 bootstrap trace vendor/genai-vanilla, README.md, docs/env-setup.md, docs/vscode-remote-access.md, docs/jupyterhub-integration.md, docs/dependency-contracts.md The repo consumed an older genai-vanilla submodule snapshot that lacked the landed ml-eng-lab JupyterHub runtime package block, while local docs still described the thekaveh-nnx[lm] image bump as pending. Fixed Bumped the submodule to 0e4e9643ac273c6f36f815a5f4b3b187876bac74, verified the pinned requirements and Dockerfile asset downloads, updated runtime docs and the contract ledger, parsed relevant YAML, and recorded the full-stack compose-config env limitation.
OM-034 Low §3.13 tests / §3.23 resilience tests/test_verify_repo.py, tests/test_rewrite_imports.py, tests/test_edit_notebook_markdown.py, tests/test_inject_smoke_test_cell.py, tests/nnx_surface/test_notebook_api_surface.py Several test helpers used subprocess.run(...) without a timeout, so a hung helper CLI or git command could block pytest until an outer job timeout. Fixed Added TEST_SUBPROCESS_TIMEOUT = 30 to the affected test helpers and adjusted the tracked-notebook fake to assert the timeout argument; focused tests and full pytest pass.
OM-035 Low §3.33 published docs surfaces docs/maintenance/overnight-2026-07-04.md, live GitHub wiki The maintenance log still grouped the wiki with stale live surfaces, but the live wiki now acts as a current signpost for ml-eng-lab and the planned Pages URL. Fixed Narrowed OM-011 to live Pages/default-branch/About drift and recorded the wiki as current as of pass 6.
OM-036 Medium §3.31 consumed contracts vendor/genai-vanilla, README.md, docs/dependency-contracts.md, runtime docs genai-vanilla upstream main advanced from the pass-6 pin 0e4e9643... to 675f1fff..., so the consumed submodule contract was behind the latest appropriate upstream state. Fixed Bumped the superproject gitlink to 675f1fffaf467a1f17ddd346e8b16fc6cbc365e0, verified the JupyterHub runtime package block and asset downloads still match the ledger, and updated README/runtime docs/dependency contracts to the new pin.
OM-037 Medium §3.6 docs / §3.31 consumed contracts CONTRIBUTING.md, notebooks/image_classification-mnist-ffnn-pytorch/README.md Contributor and per-task runtime docs still described genai-vanilla cbad341 and the defunct nnx-pytorch[lm] package name as an outstanding blocker, contradicting the current 675f1fff runtime pin. Fixed Reworded both docs to say current genai-vanilla ships thekaveh-nnx[lm]==0.2.0; older images should be pulled/rebuilt. Stale-reference sweep now shows only intentional migration history.
OM-038 Low §3.17 notebook execution / §3.32 archive hygiene notebooks/archive/codexglue_summarization/codexglue-summarization-cross-*/notebook.ipynb, tests/nnx_surface/test_notebook_api_surface.py, notebooks/archive/README.md Ten archived CodeXGLUE cross-language notebooks read historical repos/CodeXGLUE, checkpoint, BLEU, and model/test_0.* artifacts directly, so missing archive artifacts could crash the reference notebooks during review. Fixed Guarded evaluation and preview cells with explicit missing-artifact skip messages, documented the restoration requirement in the archive README, and added a static regression covering all 10 cross-language notebooks.
OM-039 Low §3.15 repository hygiene / §3.17 notebook artifacts Ignored local notebook artifact directories Local ignored duplicate root-* run directories coexisted with canonical newer nnx 0.2.0 run directories for TinyShakespeare and DPO notebooks; one notebook-local __pycache__ directory also remained. Fixed locally Removed the stale ignored root-* duplicate run dirs and notebooks/image_classification-mnist-ffnn-numpy/__pycache__/; canonical run dirs and runs/best remain. This cleanup is local because the deleted artifacts were ignored and untracked.
OM-040 Medium §3.31 consumed contracts vendor/genai-vanilla, README.md, docs/dependency-contracts.md, runtime docs genai-vanilla upstream main advanced from the pass-7 pin 675f1fff... to d2201407..., so the consumed submodule contract was again behind the latest appropriate upstream state. Fixed Bumped the superproject gitlink to d22014078041e59d076059a7704d265c79a777df, verified the JupyterHub runtime package block and asset downloads still match the ledger, and updated README/runtime docs/dependency contracts to the new pin.
OM-041 Medium §3.17 notebook execution / §3.23 resilience notebooks/archive/codexglue_summarization/codexglue-summarization-roberta-*/notebook.ipynb, tests/nnx_surface/test_notebook_api_surface.py, notebooks/archive/README.md Twelve archived RoBERTa CodeXGLUE notebooks could delete or rebuild model/, clone CodeXGLUE, download/preprocess datasets, and train/test by default when a reviewer ran the archived reference notebooks. Fixed Added ARCHIVE_RERUN_ENABLED = False opt-in guards, preservation defaults, missing-artifact previews, bounded subprocess timeouts, archive README instructions, and a red/green static regression across all 12 notebooks.
OM-042 Low §3.13 tests / §3.17 notebook artifacts tests/nnx_surface/test_notebook_api_surface.py Archive notebook helper tests discovered notebooks via filesystem globbing, so untracked scratch notebooks could accidentally enter the contract test surface and create noisy failures. Fixed Switched archive notebook discovery to git ls-files and added a regression proving untracked local scratch notebooks are ignored.
OM-043 Low §3.17 notebook execution / §3.23 resilience notebooks/archive/codexglue_summarization/codexglue-summarization-cross-*/notebook.ipynb, tests/nnx_surface/test_notebook_api_surface.py The pass-7 cross-language archive guard checked the runner and checkpoint but not the dataset path passed to subprocess, and historical subprocess calls still lacked explicit timeouts. Fixed Added a dataset-file existence check, passed the dataset path through the guarded variable, added ARCHIVE_SUBPROCESS_TIMEOUT_SECONDS, and tightened the archive guard regression.
OM-044 Low §3.12 style / §3.13 tests tests/test_verify_repo.py Two verifier tests retained unused parameters from older helper shapes, adding minor noise during maintenance review. Fixed Removed the unused tmp_path fixture from the nested docs parse test and prefixed unused fake-callback arguments with underscores; focused and full validation cover the cleanup.
OM-045 Medium §3.17 notebook execution / §3.23 resilience notebooks/archive/codexglue_summarization/codexglue-summarization-roberta-*/notebook.ipynb, tests/nnx_surface/test_notebook_api_surface.py The archived RoBERTa notebooks still copied helper files into their local src/ directories before defining ARCHIVE_RERUN_ENABLED = False, and preprocessing used os.chdir(dataset_path) without guaranteed restoration on failure. Fixed Added a failing archive regression, moved rerun flags before helper setup, made default runs use the preserved local helper snapshot without writing, changed preprocessing to subprocess.check_call(..., cwd=dataset_path, timeout=...), and reran focused/affected tests plus notebook JSON parse.
OM-046 Medium §3.17 notebook trace / §3.13 tests scripts/verify_repo.py, tests/test_verify_repo.py S2 import checking only inspected the first module in import a, b, so a valid first module could hide a missing second module and let a notebook runtime import failure pass structure verification. Fixed Added a failing temp-notebook regression for import json, definitely_missing_module_for_s2, replaced S2 extraction with AST-backed ast.Import / ast.ImportFrom walking with a syntax-fallback path, and reran focused/affected verifier tests.
OM-047 Medium §3.16 security / §3.14 CI tooling docs/dependency-contracts.md, scripts/verify_repo.py, .github/workflows/ci.yml The dependency ledger documents accepted pip-audit findings, but CI does not compare current audit output against a machine-readable accepted baseline, so new advisories could merge without an automated failure. Deferred Current pip-audit -r requirements.txt -r torch-requirements.txt still matches the documented 23 findings. A future security-hardening pass should add a checked audit-baseline artifact and CI/verifier comparison that fails only on new advisory IDs or accepted-version drift.
OM-048 Low §3.29 supply-chain reproducibility / §3.31 consumed contracts Makefile, Dockerfile, docs/dependency-contracts.md External NLP assets such as en_core_web_sm and vader_lexicon are downloaded during setup/build without an integrity-locked asset manifest. Deferred Existing runtime contract verification confirms the downloads are still declared in the pinned Dockerfile and Makefile paths. Pinning exact asset packages/checksums or adding a small mirrored fixture remains grouped with the broader reproducibility work rather than mixed into this archive/verifier pass.
OM-049 Medium §3.31 consumed contracts vendor/genai-vanilla, README.md, docs/dependency-contracts.md, runtime docs genai-vanilla upstream main advanced from the pass-9 pin d2201407... to d8ddd8e..., so the consumed submodule contract and runtime docs again overstated upstream parity. Fixed Bumped the superproject gitlink to d8ddd8e527c21ccbe78b34d72e2bb59409e52c6b, verified the JupyterHub runtime package block and NLP asset downloads still match the ledger, and updated README/runtime docs/dependency contracts to the new pin.
OM-050 Medium §3.17 notebook trace / §3.13 tests scripts/verify_repo.py, tests/test_verify_repo.py The pass-9 AST-backed S2 import extraction still fell back to first-module-only regex behavior when a notebook code cell contained IPython magic or shell syntax, so %matplotlib inline followed by import json, missing_module could hide the missing second module. Fixed Added a failing magic-plus-multi-import regression, filtered notebook-only magic/shell lines before whole-cell AST parsing, parsed fallback import lines with AST, and reran focused S2 tests plus python scripts/verify_repo.py --check all --fast.
OM-051 Medium §3.17 notebook trace / §3.13 tests scripts/verify_repo.py, tests/test_verify_repo.py S2 blanked the %%bash line of non-Python cell magics but still scanned the shell body with Python import fallback logic, so shell text such as import missing_module could create false unresolved-import findings. Fixed Added a failing %%bash regression, made S2 skip known non-Python cell-magic bodies before parsing, and reran focused S2 regressions.
OM-052 Low §3.17 notebook trace / §3.13 tests scripts/verify_repo.py, tests/test_verify_repo.py S2 ignored notebook relative imports such as from . import helper because ast.ImportFrom nodes with level > 0 and no module were discarded, even though those imports are runtime-brittle in top-to-bottom notebook execution. Fixed Added a failing relative-import regression, returned structured import records from S2 extraction, emitted explicit S2.relative_import findings, and reran focused S2 regressions.
OM-053 Low §3.31 consumed contracts / §3.11 naming vendor/genai-vanilla/services/jupyterhub/build/requirements.txt, vendor/genai-vanilla/services/jupyterhub/build/Dockerfile, docs/dependency-contracts.md The genai-vanilla upstream pin first reviewed at a22b182..., and still true at the current 10f8402... pin, contains comments using the old ml-lab repository name and URL in the JupyterHub runtime package and NLP asset blocks. The URL redirects, and the actual runtime contract is current, but the comments conflict with the local ml-eng-lab identity. Documented/deferred Recorded the limitation in the dependency ledger. Patching it requires an upstream genai-vanilla documentation commit and subsequent submodule bump; this maintenance branch did not push directly to the dependency's default branch.
OM-054 Medium §3.31 consumed contracts vendor/genai-vanilla, README.md, docs/dependency-contracts.md, runtime docs genai-vanilla upstream main advanced from the pass-11 pin d8ddd8e... to 2bee051..., so the consumed submodule contract and runtime docs again overstated upstream parity. Fixed Bumped the superproject gitlink to 2bee05134d721a152a6ea579d9a65efd7e080701, verified the JupyterHub runtime package block and NLP asset downloads still match the ledger, and updated README/runtime docs/dependency contracts to the new pin.
OM-055 High §3.17 notebook trace / §3.13 tests scripts/verify_repo.py, tests/test_verify_repo.py The new S2.relative_import guard still missed dotted relative imports such as from .helpers import VALUE because ast.ImportFrom handling checked node.module before node.level; a sibling helpers.py could then make the notebook look valid. Fixed Added a failing dotted-relative regression with a sibling helper file, changed AST extraction to treat any ImportFrom.level > 0 as relative before normal module handling, and reran all S2 import regressions.
OM-056 Low §3.14 tooling / §3.31 consumed contracts scripts/verify_repo.py, tests/test_verify_repo.py, vendor/genai-vanilla/start.sh, vendor/genai-vanilla/stop.sh E6 shellcheck coverage only iterated local scripts/*.sh, missing the consumed genai-vanilla start.sh and stop.sh entrypoints that the JupyterHub wrapper delegates to. Fixed Added a failing target-list regression, introduced _shellcheck_targets, included the consumed vendor entrypoints, and confirmed python scripts/verify_repo.py --check execution --fast plus direct shellcheck over the wrapper and vendor entrypoints pass.
OM-057 Medium §3.17 notebook trace / §3.13 tests scripts/verify_repo.py, tests/test_verify_repo.py S2.relative_import findings could be hidden when a normal same-module import appeared first, because seen_in_notebook deduped by module before the relative-import branch ran. Fixed Added a failing notebook regression with import helpers followed by from .helpers import VALUE, moved relative-import handling before normal import dedupe, and reran the S2 regression group.
OM-058 Medium §3.17 notebook trace / §3.13 tests scripts/verify_repo.py, tests/test_verify_repo.py S2's SyntaxError fallback scanned import-looking text inside multiline strings, so a string containing import missing_module could produce a false unresolved-import finding if an unrelated syntax error forced fallback parsing. Fixed Added a failing multiline-string fallback regression, blanked tokenizer STRING spans before regex fallback scanning, and reran the S2 regression group.
OM-059 Low §3.17 notebook trace / §3.13 diagnostics scripts/verify_repo.py, tests/test_verify_repo.py S2 reported zero-based line[...] locations while the rest of the verifier reports one-based human line numbers. Fixed Added a failing one-based line-location regression, changed S2 extraction to enumerate fallback lines from 1 and use AST node.lineno directly, and reran the S2 regression group.
OM-060 Medium §3.14 tooling / §3.31 consumed contracts scripts/verify_repo.py, tests/test_verify_repo.py, docs/dependency-contracts.md, vendor/genai-vanilla/bootstrapper/_run.sh E6 covered the consumed vendor start.sh and stop.sh wrappers but missed their shared bootstrapper/_run.sh dispatcher, which is executed by both entrypoints. Fixed Added a failing target-list regression for _run.sh, included the dispatcher in _shellcheck_targets, updated the dependency contract checklist, and confirmed python scripts/verify_repo.py --check execution --fast plus direct shellcheck pass.
OM-061 Medium §3.31 consumed contracts vendor/genai-vanilla, README.md, docs/dependency-contracts.md, runtime docs genai-vanilla upstream main advanced from the pass-13 pin 2bee051... to a22b182..., so the consumed submodule contract and runtime docs again overstated upstream parity. Fixed Bumped the superproject gitlink to a22b182a0f0cd1bb0be3599a7710d87890491eb8, verified the upstream delta changed Browserless research docs/tests only, re-checked the JupyterHub runtime package block and NLP asset downloads, and updated README/runtime docs/dependency contracts to the new pin.
OM-062 Medium §3.14 tooling / §3.31 consumed contracts scripts/verify_repo.py, tests/test_verify_repo.py, docs/dependency-contracts.md, vendor/genai-vanilla/services/jupyterhub/build/scripts/startup.sh E6 shellcheck coverage followed the consumed genai-vanilla wrapper/dispatcher path but missed the JupyterHub image startup.sh copied and used by the consumed Dockerfile. Fixed Added a failing target-list regression for startup.sh, included the image entrypoint in _shellcheck_targets, updated the dependency contract checklist, and confirmed the focused regression plus direct shellcheck pass.
OM-063 Medium §3.32 examples/library-fit docs notebooks/quantization-mnist-ffnn-pytorch/README.md The quantization notebook README presented a papermill command as a path in ml-eng-lab's pinned environment while the same section correctly said the notebook cannot execute under pinned torch==2.4.1. Fixed Reworded the run instructions to state the notebook is manual-only outside the pinned genai-vanilla/CI environment and to run papermill only from a side environment with torch>=2.5 and torchao>=0.17.
OM-064 Medium §3.14 tooling / §3.31 consumed contracts scripts/verify_repo.py, tests/test_verify_repo.py, .github/workflows/ci.yml E6 treated required consumed vendor shellcheck targets as optional existing files, so a checkout without initialized submodules could pass make verify without checking genai-vanilla entrypoints. Fixed Added a failing missing-target regression, split required vendor targets from discovered local scripts, emitted E6.shellcheck_target_missing for absent vendor targets, and configured the verify-repo CI checkout to initialize submodules.
OM-065 Low §3.8 documentation link hygiene CHANGELOG.md, scripts/verify_repo.py, tests/test_verify_repo.py A historical changelog before/after snippet rendered a sibling-relative ../nnx example as a live relative link to a removed sibling path. Fixed Reworded the snippet so the historical source text renders literally, added S3.repo_escape_link to reject repo-escaping relative links, and added a regression for sibling-directory links.
OM-066 Low §3.17 notebook trace / §3.31 PyG contract scripts/verify_repo.py, tests/test_verify_repo.py, Reddit phase-3 notebooks Known runtime-container-only torch_sparse imports in four Tier-C notebooks produced recurring local verifier warnings even though the dependency belongs to the documented full runtime. Fixed Added an S2 regression for acknowledged runtime-only imports and skipped configured _RUNTIME_ONLY_MODULES during structure import resolution; python scripts/verify_repo.py --check all --fast now reports 0 findings locally.
OM-067 Medium §3.31 consumed contracts vendor/genai-vanilla, README.md, docs/dependency-contracts.md, runtime docs genai-vanilla upstream main advanced from the pass-15 pin a22b182... to 448333d..., so the consumed submodule contract and current runtime docs again overstated upstream parity. Fixed Bumped the superproject gitlink to 448333d3b1a530fafd76d224ee1066181de8fac4, verified the upstream delta changed Supabase research docs/tests only after the prior Browserless delta, re-checked the JupyterHub runtime package block and NLP asset downloads, and updated README/runtime docs/dependency contracts to the new pin.
OM-068 Medium §3.13 tests / §3.14 CI tooling .github/workflows/ci.yml, Makefile, CONTRIBUTING.md, tests/ CI runs the NNx surface tests and verifier, but not the full local make test contract, leaving helper/tooling tests outside the required per-PR CI gate. Deferred Local full-suite validation remains run and recorded during maintenance passes. A future CI-hardening pass should add a separate full make test job or a scoped non-tests/nnx_surface helper-test job with runtime/cost expectations documented.
OM-069 Low §3.17 notebook trace / §3.31 NNx public API fit Active notebooks with from nnx.nn..., from nnx.vis_utils..., and from nnx.seeding... imports Several active notebooks still teach private-ish nnx package paths even though the same symbols are available from the top-level nnx public facade. Deferred Verified the top-level exports exist for the relevant symbols, but the finding includes Tier-C Reddit phase3 notebooks whose code cells are intentionally source-locked by E5 against pre-cleanup-baseline. Defer to a coordinated notebook public-import modernization pass that updates or consciously relaxes that baseline contract rather than mixing it into this submodule/docs/tooling pass.
OM-070 Low §3.17 archive execution trace notebooks/archive/codexglue_summarization/codexglue-summarization-cross-*/notebook.ipynb Archived CodeXGLUE cross-language notebooks computed repo_path one level above the notebook directory but printed a restore hint telling readers to restore ./repos/CodeXGLUE from the notebook directory. Fixed Updated all ten restore hints to print the actual computed repo_path, preserving one-line notebook diffs and validating notebook JSON parse.
OM-071 Low §3.32 examples/library-fit docs notebooks/text_classification-agnews-spacy-mlp-pytorch/notebook.ipynb The AG-News discussion still pointed readers to the removed peft-mnist-to-fmnist-dora-vs-lora/ folder name instead of the moved notebooks/peft-mnist-to-fmnist-dora-vs-lora-pytorch/ task. Fixed Replaced the stale inline path with a real relative Markdown link to the current PEFT notebook folder and confirmed the diff is a single markdown-cell line.
OM-072 Medium §3.13 tests / §3.15 repo hygiene pyproject.toml, vendor/genai-vanilla, tests/ Bare python -m pytest from the repo root collected vendored genai-vanilla tests and failed during collection even though make test scopes to local tests/. Fixed Added pytest testpaths = ["tests"] and norecursedirs for vendor/archive/venv paths; root collect-only now reports the intended 408 repo tests without vendored collection errors.
OM-073 Low §3.13 tests / §3.15 repo hygiene tests/test_numpy_layers.py The NumPy layer test inserted the notebook helper directory at sys.path[0] at import time and never removed it, allowing later imports such as utils to resolve to notebook helpers during broad pytest collection. Fixed Wrapped the notebook-helper imports in a temporary import-path context so the path is removed after loading the layer classes; focused and full tests pass.
OM-074 Low §3.6 code comment accuracy / §3.15 hygiene scripts/rewrite_imports.py A maintenance comment said call-site rewrites include commented-out lines, contradicting the tokenizer behavior and tests that intentionally preserve comments and strings. Fixed Reworded the comment to say executable code lines are rewritten while comments and string literals are preserved.
OM-075 Low §3.6 docs / §3.31 consumed contracts notebooks/image_classification-mnist-ffnn-pytorch/README.md The per-task known-issues guidance still told users that images older than genai-vanilla 2bee051 could carry the defunct nnx-pytorch[lm] package, even though the current runtime pin is 448333d. Fixed Updated the stale pin to 448333d; python scripts/verify_repo.py --check all --fast and docs build pass.
OM-076 Low §3.31 consumed contracts / §3.15 maintenance hygiene docs/maintenance/overnight-2026-07-04.md OM-053 wording described the stale upstream ml-lab comments as tied to the earlier a22b182 pin even after the current 448333d bump re-verified the same deferred vendor issue. Fixed Reworded OM-053 to distinguish the first-reviewed pin from the current pin and reran verifier/docs validation.
OM-077 Low §3.31 consumed contracts / §3.8 documentation indexing docs/FINDINGS-VENDOR.md The vendor findings index still said there were no findings even though the dependency ledger now documents deferred stale ml-lab comments inside the genai-vanilla JupyterHub runtime files. Fixed Added a genai-vanilla vendor finding that cross-links the dependency-contract ledger; docs verifier and docs build pass.
OM-078 Medium §3.14 tooling / §3.31 consumed contracts scripts/verify_repo.py, tests/test_verify_repo.py Required consumed vendor shell entrypoints were only checked when shellcheck was installed, so a machine missing shellcheck could also miss absent submodule entrypoints. Fixed Moved required-target existence checks before the optional shellcheck probe and added a regression for missing vendor targets when shellcheck is absent; focused and full tests pass.
OM-079 Medium §3.29 build reproducibility / §3.14 CI tooling .github/workflows/ci.yml, .github/workflows/pages.yml, docs-requirements.txt, docs/dependency-contracts.md Documentation-only CI and Pages jobs installed the full ML runtime requirements.txt, letting unrelated Torch/PyG/NNx resolver behavior affect MkDocs builds. Fixed Added docs-requirements.txt, switched docs jobs to install/cache it, documented the split, and verified pip-audit -r docs-requirements.txt, docs build, workflow YAML parse, and full tests.
OM-080 Medium §3.31 consumed contracts vendor/genai-vanilla, README.md, CONTRIBUTING.md, runtime docs, docs/dependency-contracts.md genai-vanilla upstream main advanced from the pass-17 pin 448333d... to 0bc3abd..., so the consumed submodule contract and current runtime docs again overstated upstream parity. Fixed Bumped the superproject gitlink to 0bc3abd3cafb35b340f90c4efa89d64375ac9152, verified the upstream delta changed OpenLIT research docs/tests only, re-checked the JupyterHub runtime package block and NLP asset downloads, and updated current runtime docs/dependency contracts to the new pin.
OM-081 Low §3.31 consumed contracts / §3.15 maintenance hygiene docs/maintenance/overnight-2026-07-04.md The pass history and OM-053 entry still described the current genai-vanilla pin as 448333d after pass 18 consumed 0bc3abd. Fixed Added the pass-18 row and validation evidence, and updated OM-053 to distinguish the first-reviewed stale-comment finding from the current 0bc3abd pin.
OM-082 Medium §3.17 archive execution trace / §3.23 resilience notebooks/archive/codexglue_summarization/codexglue-summarization-*/notebook.ipynb, tests/nnx_surface/test_notebook_api_surface.py All 22 archived CodeXGLUE notebooks derived notebook_path from os.path.abspath(os.curdir), so model, source, and restored CodeXGLUE paths could point at the wrong directory when the kernel CWD was repo root or launcher-controlled. Fixed Added a failing static guard, anchored each archive notebook to its explicit archived folder name by searching up from the current working directory, and verified all 22 CodeXGLUE notebooks parse.
OM-083 Medium §3.17 archive execution trace / §3.23 resilience notebooks/archive/codexglue_summarization/codexglue-summarization-cross-*/notebook.ipynb, tests/nnx_surface/test_notebook_api_surface.py The ten cross-language CodeXGLUE notebooks could still run write-capable test subprocesses by default when historical checkout/checkpoint files existed, despite archive docs requiring explicit rerun opt-in. Fixed Added a failing static guard, inserted ARCHIVE_RERUN_ENABLED = False, and made cross-language test evaluation skip unless explicitly enabled.
OM-084 Medium §3.14 tooling / §3.13 tests scripts/verify_repo.py, tests/test_verify_repo.py verify_repo.py --repo-root <other-repo> still used this checkout's import-time verify_repo_config.yaml, so alternate repos with their own config were checked against ml-eng-lab's active task list. Fixed Added a failing temp-repo config regression, made main() activate the target repo's config when present, and preserved default config behavior for existing fixture repos without a config.
OM-085 Low §3.14 tooling / §3.13 tests scripts/rewrite_imports.py, tests/test_rewrite_imports.py rewrite_imports.py missed parenthesized deprecated parameter imports when the symbol line had an inline comment, leaving GraphAttNNParams, # ... in migrated notebook code. Fixed Added a failing parenthesized-inline-comment regression and normalized import symbols by stripping inline comments before deprecated-symbol matching.
OM-086 Medium §3.31 consumed contracts vendor/genai-vanilla, README.md, CONTRIBUTING.md, runtime docs, docs/dependency-contracts.md genai-vanilla upstream main advanced from the pass-18 pin 0bc3abd... to 2997143..., so the consumed submodule contract and current runtime docs again overstated upstream parity. Fixed Bumped the superproject gitlink to 2997143758f58f4c40ecd6e258fa8422942cb7cd, verified the upstream delta changed live-trading research docs/tests only, re-checked the JupyterHub runtime package block and NLP asset downloads, and updated current runtime docs/dependency contracts to the new pin.
OM-087 Low §3.17 notebook execution trace / §3.23 reproducibility Active notebooks under notebooks/ Twelve active notebooks still carried stale local kernelspec display names or Python versions such as base, Python 3.8.12, 3.10.x, or 3.11.6, despite the documented runtime being the generic python3 / Python 3.11 environment. Fixed Normalized active notebook metadata to kernelspec.name=python3, display name Python 3, and Python 3.11.0; verified all 29 active notebooks match without re-executing Tier-C outputs.
OM-088 Medium §3.14 tooling / §3.13 tests scripts/rewrite_imports.py, tests/test_rewrite_imports.py rewrite_imports.py missed deprecated Params imports when a parenthesized import closed on the same symbol line, leaving cases such as GraphAttNNParams) unchanged. Fixed Added a failing same-line-closing regression and taught the parenthesized-import state to strip closing parens before deprecated-symbol matching.
OM-089 Low §3.14 tooling / §3.13 tests scripts/rewrite_imports.py, tests/test_rewrite_imports.py Old from common.nn_model import NNModel, NNTrainParams # ... imports skipped the intended split rule because the regex only accepted trailing whitespace. Fixed Added a failing inline-comment split regression and allowed the split patterns to preserve trailing comments while emitting the modern NNModel and NNTrainParams import paths separately.
OM-090 Low §3.14 tooling / §3.13 tests scripts/verify_repo.py, tests/test_verify_repo.py S2 unresolved-import checks covered import and from statements but not literal dynamic imports like importlib.import_module("missing") or __import__("missing"). Fixed Added a failing dynamic-literal regression and extended the AST walk to report literal dynamic import module names with one-based line locations.
OM-091 Low §3.6 docs / §3.11 naming docs/superpowers/*, runtime docs A few preserved/generated docs still pointed at the old ml-lab repository slug or pre-notebooks/ nbviewer paths, and current runtime docs still referenced the previous genai-vanilla pin. Fixed Updated tracked current docs to ml-eng-lab and 2997143; refreshed old nbviewer links in local superpowers docs to the notebooks/ layout.
OM-092 Medium §3.14 tooling / §3.13 tests scripts/rewrite_imports.py, tests/test_rewrite_imports.py rewrite_imports.py treated every from ... import ( opener as multiline and dropped valid single-line parenthesized imports such as from ... import (GraphAttNN, GraphAttNNParams). Fixed Added failing single-line parenthesized import regressions and normalized those imports before the existing deprecated-Params rewrite path runs.
OM-093 Low §3.14 tooling / §3.13 tests scripts/verify_repo.py, tests/test_verify_repo.py S2 literal dynamic-import checks missed common importlib alias forms such as from importlib import import_module and import importlib as il. Fixed Added a failing alias regression and tracked simple importlib/import_module aliases during the AST walk.
OM-094 Low §3.8 documentation indexing / §3.15 maintenance hygiene Ignored local docs/superpowers/plans/*.md scratch docs Excluded superpowers plan docs still carried stale relative links from the pre-notebooks/ layout. They are ignored and not part of the published/docs verifier surface, but they were noisy during fresh review. Local ignored cleanup Mechanically rewrote local ignored plan links; a local checker over docs/superpowers/plans/*.md went from 53 broken local links to 0. The ignored scratch docs were not force-added to the branch.
OM-095 Medium §3.31 consumed contracts vendor/genai-vanilla, README.md, CONTRIBUTING.md, runtime docs, docs/dependency-contracts.md genai-vanilla upstream main advanced from the pass-19 pin 2997143... to 1631344..., so the consumed submodule contract and current runtime docs again overstated upstream parity. Fixed Bumped the superproject gitlink to 163134451a19d024e0e1c0df51139fd8c0a2ca52, verified the upstream delta changed FinRL FinGPT research docs/tests only, re-checked the JupyterHub runtime package block and NLP asset downloads, and updated current runtime docs/dependency contracts to the new pin.
OM-096 Medium §3.14 tooling / §3.31 consumed contracts scripts/verify_repo.py, tests/test_verify_repo.py, vendor/genai-vanilla The verifier did not flag required submodules whose working tree commit differed from the staged superproject gitlink, allowing a dirty submodule bump to leave docs/verifier state mismatched. Fixed Added E6.submodule_dirty for required submodules, covered it with a temp-repo regression, and confirmed the staged genai-vanilla gitlink is clean at 1631344.
OM-097 Low §3.17 notebook trace / §3.13 tests scripts/verify_repo.py, tests/test_verify_repo.py S2's SyntaxError fallback path still missed literal dynamic imports through importlib aliases such as from importlib import import_module; import_module("missing"), even though the AST path handled them. Fixed Added a failing fallback-alias regression, tracked importlib/import_module aliases while scanning fallback lines, and reported literal alias calls with one-based locations.
OM-098 Medium §3.14 tooling / §3.13 tests scripts/rewrite_imports.py, tests/test_rewrite_imports.py rewrite_imports.py treated each notebook source list element as a physical line, so a multi-line chunk could be dropped or mis-rewritten during deprecated-import migration. Fixed Added a failing chunked-source regression and split list-source chunks into physical lines with splitlines(keepends=True) before applying the existing rewrite rules.
OM-099 Low §3.15 maintenance hygiene / §3.31 consumed contracts docs/maintenance/overnight-2026-07-04.md OM-053 still described the stale upstream ml-lab comments as present at the current 2997143 pin after pass 21 consumed 1631344. Fixed Updated OM-053 to name the current 1631344 pin; the broader upstream-comment limitation remains documented/deferred.
OM-100 Medium §3.17 notebook trace / §3.13 tests scripts/verify_repo.py, tests/test_verify_repo.py S2's SyntaxError fallback tracked single-line importlib aliases but missed parenthesized multiline alias declarations before a literal dynamic import call. Fixed Added a failing multiline-alias fallback regression and parsed parenthesized from importlib import (...) fallback blocks as one statement before scanning later dynamic import calls.
OM-101 Medium §3.14 tooling / §3.13 tests scripts/rewrite_imports.py, tests/test_rewrite_imports.py rewrite_imports.py still missed valid notebook source lists whose chunks split a single logical line, such as ["from common.", "nn_model import NNModel\\n"]. Fixed Added a failing split-logical-line regression and joined notebook source chunks before splitting into physical lines for rewriting.
OM-102 Medium §3.14 tooling / §3.31 consumed contracts scripts/verify_repo.py, tests/test_verify_repo.py, vendor/genai-vanilla E6.submodule_dirty caught gitlink mismatches, uninitialized submodules, and merge-conflict states, but not ordinary modified or untracked files inside required submodule worktrees. Fixed Added a failing modified-submodule-worktree regression and made E6 inspect git status --porcelain inside each required submodule after the gitlink status is clean.
OM-103 Medium §3.31 consumed contracts vendor/genai-vanilla, README.md, CONTRIBUTING.md, runtime docs, docs/dependency-contracts.md genai-vanilla upstream main advanced from the pass-21 pin 1631344... to b96a292..., so the consumed submodule contract and current runtime docs again overstated upstream parity. Fixed Bumped the superproject gitlink to b96a2924b5d30aa30eddb2fa43f9b7a47fc81bcb, verified the upstream delta changed heavy 3D infrastructure research docs/tests only, re-checked the JupyterHub runtime package block and NLP asset downloads, and updated current runtime docs/dependency contracts to the new pin.
OM-104 Medium §3.8 documentation indexing / §3.31 consumed contracts scripts/verify_repo.py, tests/test_verify_repo.py, docs/dependency-contracts.md, vendor/genai-vanilla The dependency-ledger verifier reconciled audit counts but did not compare the ledger's declared genai-vanilla SHA with the superproject gitlink, so a docs-only pin bump could pass clean CI after checkout reset the submodule to the old gitlink. Fixed Added D10.dependency_ledger_submodule_sha, comparing the ledger SHA to the index gitlink from git ls-files --stage, with a failing temp-repo regression.
OM-105 Medium §3.17 notebook trace / §3.13 tests scripts/verify_repo.py, tests/test_verify_repo.py S2's SyntaxError fallback handled multiline importlib alias declarations but still missed multiline literal dynamic import calls such as importlib.import_module(\\n \"missing\"\\n). Fixed Added a failing multiline dynamic-call fallback regression and generalized fallback statement reconstruction for balanced parenthesized statements.
OM-106 Low §3.13 tests / §3.31 consumed contracts tests/test_verify_repo.py The pass-22 required-submodule worktree regression did not assert that git status --porcelain -- . runs with the submodule as cwd, so a future regression to checking the superproject root could pass the test. Fixed Added a cwd assertion to the test double; it passed against the current implementation and now guards the intended working-directory contract.
OM-107 Medium §3.31 consumed contracts vendor/genai-vanilla, README.md, CONTRIBUTING.md, runtime docs, docs/dependency-contracts.md genai-vanilla upstream main advanced from the pass-23 pin b96a292... to ba21661..., so the consumed submodule contract and current runtime docs again overstated upstream parity. Fixed Bumped the superproject gitlink to ba21661e8a63b3727b9c4a14eaf5e61262d4b48e, verified the upstream delta changed voice-stack research docs/tests only, re-checked the JupyterHub runtime package block and NLP asset downloads, and updated current runtime docs/dependency contracts to the new pin.
OM-108 Medium §3.8 documentation indexing / §3.31 consumed contracts scripts/verify_repo.py, tests/test_verify_repo.py, docs/dependency-contracts.md D10 compared the ledger SHA to the superproject gitlink only when it could parse a valid currently pins tree entry SHA, so removing or malformed-rewording the required SHA sentence let the dependency ledger fail open. Fixed Added a failing missing-SHA regression and made D10 emit D10.dependency_ledger_submodule_sha when a genai-vanilla ledger mentions the submodule without a parseable 40-character pinned tree-entry SHA.
OM-109 Medium §3.17 notebook trace / §3.13 tests scripts/verify_repo.py, tests/test_verify_repo.py S2's SyntaxError fallback reconstructed parenthesized multiline statements but still missed backslash-continued multi-imports such as import json, \\ followed by a missing module on the next line. Fixed Added a failing backslash-continuation regression and extended fallback statement reconstruction to join explicit line continuations before scanning imports.
OM-110 Medium §3.14 tooling / §3.13 tests scripts/rewrite_imports.py, tests/test_rewrite_imports.py rewrite_imports.py rewrote deprecated Params call sites one physical line at a time, so valid explicit-continuation calls such as GraphAttNNParams \\ followed by (...) kept the stale constructor name after the import was migrated. Fixed Added a failing backslash-continuation call-site regression, made call-site token offsets work across multiline logical statements, and added a continuation-aware second pass before NNParams import injection.
OM-111 Medium §3.8 documentation indexing / §3.31 consumed contracts scripts/verify_repo.py, tests/test_verify_repo.py, docs/dependency-contracts.md D10 failed closed for a missing ledger SHA but still failed open when git ls-files --stage -- vendor/genai-vanilla returned no parseable submodule gitlink, leaving the ledger SHA unverified. Fixed Added a failing missing-gitlink regression and made D10 emit D10.dependency_ledger_submodule_sha with gitlink_sha=None when the superproject gitlink cannot be parsed.
OM-112 Medium §3.31 consumed contracts vendor/genai-vanilla, README.md, CONTRIBUTING.md, runtime docs, docs/dependency-contracts.md genai-vanilla upstream main advanced from the pass-24 pin ba21661... to 329f883..., so the consumed submodule contract and current runtime docs again overstated upstream parity before the pass-25 commit. Fixed Bumped the superproject gitlink to 329f883139f9b101ef923376b84d5d9199c47b56, verified the upstream delta changed Honcho research docs/tests only, re-checked the JupyterHub runtime package block and NLP asset downloads, and updated current runtime docs/dependency contracts to the new pin.
OM-113 Low §3.6 docs / §3.15 maintenance hygiene docs/maintenance/overnight-2026-07-04.md The validation log appended pass-17/pass-18 evidence after pass 27, so chronological review of validation evidence jumped backward from pass 27 to pass 18. Fixed Moved the pass-17/pass-18 validation evidence to its chronological position before pass 19 and recorded the repair in the pass-28 validation log.
OM-114 Medium §3.14 tooling / §3.17 notebook execution trace scripts/rewrite_imports.py, tests/test_rewrite_imports.py rewrite_imports.py inserted a required NNParams import at the top of every migrated cell, which could move code above a first-line Jupyter cell magic such as %%time and change the cell's execution semantics. Fixed Added a failing cell-magic regression and changed the import insertion index so first-line %% magics remain line 1 while the generated import is inserted immediately after the magic.
OM-115 Medium §3.31 consumed contracts vendor/genai-vanilla, README.md, CONTRIBUTING.md, runtime docs, docs/dependency-contracts.md genai-vanilla upstream main advanced from the pass-25 pin 329f883... to c2ffe8d..., so the consumed submodule contract and current runtime docs again overstated upstream parity before the pass-29 commit. Fixed Bumped the superproject gitlink to c2ffe8d10f5f21c549b411d87861c83e518073ba, verified the upstream delta changed Redis Stack/RedisInsight research docs and a bootstrapper deferral test only, re-checked the JupyterHub runtime package block and NLP asset downloads, and updated current runtime docs/dependency contracts to the new pin.
OM-116 Low §3.6 docs / §3.17 notebook artifacts README.md The README said each active experiment directory contains gitignored data/ and runs/ directories, but a clean checkout does not guarantee those runtime-created folders exist for every task. Fixed Reworded the overview to say task directories contain notebook(s) and README, with gitignored data/ and runs/ directories created as needed by downloads and training/evaluation runs.
OM-117 Medium §3.14 tooling / §3.13 tests scripts/rewrite_imports.py, tests/test_rewrite_imports.py rewrite_imports.py dropped valid kept symbols when a parenthesized import closing line mixed a deprecated Params symbol with another import member, such as GraphAttNN, GraphAttNNParams). Fixed Added failing mixed-closing-line regressions for deprecated-last and deprecated-first order, then split parenthesized member lines on comma fragments so only deprecated Params are dropped and valid symbols are preserved.
OM-118 Medium §3.31 consumed contracts vendor/genai-vanilla, README.md, CONTRIBUTING.md, runtime docs, docs/dependency-contracts.md genai-vanilla upstream main advanced from the pass-29 pin c2ffe8d... to 10f8402..., so the consumed submodule contract and current runtime docs again overstated upstream parity before the pass-30 commit. Fixed Bumped the superproject gitlink to 10f840252404eb5399550f96fbb560153f1a47c7, verified the upstream delta changed Perplexica/Vane research docs and a bootstrapper deferral test only, re-checked that consumed JupyterHub runtime files were unchanged, and updated current runtime docs/dependency contracts to the new pin.
OM-119 Low §3.14 tooling / §3.13 tests scripts/rewrite_imports.py, tests/test_rewrite_imports.py rewrite_imports.py did not count an existing parenthesized NNParams import when the NNParams) member closed the import on the same line, so later deprecated call-site rewriting injected a duplicate bare NNParams import. Fixed Added a failing same-line parenthesized NNParams regression and counted kept members from canonical parenthesized nn_params imports before deciding whether to inject a replacement import.
OM-120 Medium §3.14 tooling / §3.13 tests scripts/rewrite_imports.py, tests/test_rewrite_imports.py rewrite_imports.py entered parenthesized-import mode when it saw from ... import ( but ignored deprecated Params symbols already present on that opener line, leaving shapes such as from ... import (GraphAttNNParams, unchanged. Fixed Added a failing opener-line member regression and normalized opener lines into a plain opener plus synthetic member text that flows through the existing parenthesized member rewriter.
OM-121 Medium §3.14 tooling / §3.13 tests scripts/rewrite_imports.py, tests/test_rewrite_imports.py rewrite_imports.py rewrote any deprecated Params token followed by (, including qualified attributes and class/function declarations such as legacy.GraphAttNNParams(...), class GraphAttNNParams(...), and def GraphConvNNParams(...). Fixed Added a failing qualified/declaration regression and skipped replacements when the previous significant token is ., class, or def, preserving comments/strings and bare constructor rewrites.
OM-122 Medium §3.14 tooling / §3.13 tests scripts/rewrite_imports.py, tests/test_rewrite_imports.py Parenthesized import blocks without deprecated Params symbols were normalized through the migration rewriter, dropping comment-only lines and inline comments during an intended no-op run. Fixed Added a failing no-op parenthesized-import preservation regression and kept raw parenthesized import blocks unchanged unless a deprecated Params symbol is actually removed.
OM-123 Medium §3.17 notebook trace / §3.13 tests scripts/verify_repo.py, tests/test_verify_repo.py S2 collapsed dotted import paths to the top-level package before checking importability, so json.definitely_missing passed whenever json existed. Fixed Added a failing dotted-submodule regression and preserved full dotted paths for import, from, and literal dynamic imports while retaining root-module allowlisting for runtime-only packages.
OM-124 Low §3.14 tooling / §3.23 resilience scripts/rewrite_imports.py, tests/test_rewrite_imports.py rewrite_imports.py printed SKIP (not found) for missing explicit input paths but still exited 0, making typoed migration commands look successful. Fixed Added a failing missing-path CLI regression and made the command return 1 when any requested input path is absent.
OM-125 Low §3.17 notebook execution / §3.6 docs README.md, Makefile, active notebook outputs Tier-B/C smoke targets write executed notebooks to /tmp/ml-smoke but run papermill from task directories, so ignored task-local ./data or ./runs artifacts can be created even when source outputs are preserved; committed output text such as Run saved to ./runs/... could imply clean-checkout artifacts exist. Fixed Documented that smoke output notebooks live under /tmp/ml-smoke while runtime artifacts remain task-local and ignored by design.
OM-126 Medium §3.29 supply-chain reproducibility / §3.13 tests .github/workflows/*.yml, docs/dependency-contracts.md, scripts/verify_repo.py, tests/test_verify_repo.py Workflow actions were manually SHA-pinned and documented, but no verifier check enforced full-SHA refs or reconciled workflow refs/comments with the dependency ledger. Fixed Added D10 workflow action-pin validation with regressions for tag refs, missing ledger rows, and current clean workflow pins.
OM-127 Medium §3.29 supply-chain reproducibility / §3.13 tests .github/workflows/*.yaml, scripts/verify_repo.py, tests/test_verify_repo.py D10 workflow action-pin validation scanned .yml workflows only, but GitHub Actions also executes .yaml, so a future unpinned .yaml workflow could bypass the verifier. Fixed Added a failing .yaml workflow action-pin regression and scanned both .yml and .yaml workflow files.
OM-128 Medium §3.14 tooling / §3.13 tests scripts/rewrite_imports.py, tests/test_rewrite_imports.py rewrite_imports.py removed deprecated Params imports but only rewrote constructor calls, leaving non-call references such as ParamsClass = GraphAttNNParams or isinstance(..., GraphAttNNParams) stale and undefined. Fixed Added a failing non-call reference regression and broadened token-based replacement to unqualified executable deprecated Params names while preserving qualified attributes, comments/strings, and declaration names.
OM-129 Medium §3.31 consumed contracts / §3.14 tooling docs/dependency-contracts.md The genai-vanilla upgrade checklist said to run docker compose config with the wrapper-provided environment, but the command also needs vendor/genai-vanilla/.env.example; without that env file, compose expands many consumed service variables to blanks and fails before producing a config. Fixed Updated the checklist with the exact passing docker compose --env-file vendor/genai-vanilla/.env.example -f vendor/genai-vanilla/docker-compose.yml -f deploy/genai-vanilla-jupyterhub.override.yml config command and verified the no-env command fails while the env-file command passes.
OM-130 Medium §3.14 tooling / §3.13 tests scripts/rewrite_imports.py, tests/test_rewrite_imports.py rewrite_imports.py normalized every single-line parenthesized import, so a no-op input such as from some.module import (UsefulSymbol) was rewritten even though it contained no deprecated Params symbol or path migration. Fixed Added a failing no-op single-line parenthesized import regression and made single-line normalization return unchanged unless a deprecated Params symbol is present.
OM-131 Medium §3.14 tooling / §3.13 tests scripts/rewrite_imports.py, tests/test_rewrite_imports.py When removing a deprecated Params member from a parenthesized import block, rewrite_imports.py rebuilt kept member lines and dropped comment-only lines, deleting useful comments such as GraphAttNN, # keep this inline note. Fixed Added a failing comment-preservation regression and preserved non-deprecated member/comment lines verbatim unless the physical line itself needs deprecated-symbol removal.
OM-132 Medium §3.14 tooling / §3.13 tests scripts/verify_repo.py, scripts/rewrite_imports.py, tests/test_verify_repo.py, tests/test_rewrite_imports.py S5 and rewrite_imports.py only recognized common imports when common started the import statement, so a valid multi-import such as import os, common.utils could bypass verification and remain unmigrated. Fixed Added failing Python/notebook S5 regressions plus a notebook rewrite regression, reused AST import extraction for S5, and rewrote common aliases inside comma-separated import lists.
OM-133 High §3.14 tooling / §3.17 notebook trace scripts/rewrite_imports.py, tests/test_rewrite_imports.py Import and deprecated Params rewrites could mutate triple-quoted string bodies, rewriting historical text such as from common.nn_model import NNModel and injecting NNParams imports for non-executable prose. Fixed Added a failing multiline-string preservation regression and skipped rewrite processing for lines covered by multiline string tokens.
OM-134 Medium §3.14 tooling / §3.17 notebook trace scripts/rewrite_imports.py, tests/test_rewrite_imports.py The pass-36 comma-separated import rewrite also ran inside non-Python cell magics such as %%bash, changing shell text that should not be treated as Python imports. Fixed Added a failing non-Python cell-magic regression and made rewrite_lines return non-Python cell-magic bodies unchanged.
OM-135 Medium §3.14 tooling / §3.13 tests scripts/rewrite_imports.py, tests/test_rewrite_imports.py Existing aliased NNParams imports were tracked by binding name while needed imports were tracked as NNParams as Alias, so dropping an aliased deprecated Params import could inject a duplicate identical alias import. Fixed Added a failing duplicate-aliased-import regression and compared existing and needed NNParams imports using the same canonical import-requirement text.
OM-136 Medium §3.17 notebook trace / §3.13 tests scripts/verify_repo.py, tests/test_verify_repo.py S2 fallback statement reconstruction counted parentheses in comments, so a parenthesized from importlib import (...) line with ) in a comment could prevent later literal dynamic import aliases from being checked. Fixed Added a failing fallback regression with a comment parenthesis and made fallback parenthesis balance token-aware.
OM-137 Low §3.14 tooling / §3.13 tests scripts/rewrite_imports.py, tests/test_rewrite_imports.py, docs/maintenance/overnight-2026-07-04.md Rewritten parenthesized import blocks dropped trailing comments on same-line closing parentheses, and pass 7 issue accounting overstated historical issue totals by three. Fixed Added a failing closing-paren comment regression, preserved the original closing-paren comment suffix, and corrected pass 7's issue count so pass-history totals reconcile with the OM issue log.
OM-138 Medium §3.14 tooling / §3.13 tests scripts/rewrite_imports.py, tests/test_rewrite_imports.py Deprecated Params name rewriting also changed local binding positions such as function parameters, assignment targets, and loop targets, silently changing local API or variable semantics. Fixed Added a failing binding-position regression and skipped deprecated-name rewrites for symbols that are local bindings anywhere in the cell.
OM-139 Low §3.14 tooling / §3.13 tests scripts/rewrite_imports.py, tests/test_rewrite_imports.py from common import utils remained unchanged by the notebook migration script even though S5 correctly treats common as a forbidden module. Fixed Added a failing from common import utils regression and mapped it to from nnx import utils.
OM-140 Medium §3.17 notebook trace / §3.13 tests scripts/verify_repo.py, tests/test_verify_repo.py S1 checked raw notebooks for missing cell IDs but did not validate the raw notebook schema, allowing invalid nbformat minor/cell-ID combinations to pass structure verification. Fixed Added a failing schema-validation regression and made S1 emit S1.schema for raw notebook schema validation failures while preserving the raw missing-ID guard.
OM-141 Medium §3.17 notebook artifacts notebooks/node_classification-reddit-gnn-pyg/phase2-model-selection-notebook*.ipynb, notebooks/node_classification-reddit-gnn-pyg/phase3-main-model-training-and-eval-notebook*.ipynb Eight active Reddit phase2/phase3 notebooks contained cell id fields while declaring nbformat_minor: 2, which is schema-invalid because cell IDs require nbformat 4.5+. Fixed Updated those notebooks to nbformat_minor: 5; all 51 notebooks pass nbformat.validate.
OM-142 Medium §3.14 tooling / §3.13 tests scripts/rewrite_imports.py, tests/test_rewrite_imports.py Pass-38's cell-wide deprecated Params binding protection could suppress legitimate imported-name reads when a later function parameter or local binding reused the same deprecated name, leaving stale GraphAttNNParams references after the import was migrated. Fixed Added a failing mixed imported/local binding regression and replaced name-wide protection with token-position-aware protection for local binding scopes.
OM-143 Medium §3.17 notebook artifacts / §3.13 tests scripts/verify_repo.py, tests/test_verify_repo.py, notebooks/archive/codexglue_summarization/*/notebook.ipynb S1 raw cell-ID/schema validation only iterated configured active task notebooks, so archive notebooks under notebooks/archive/ bypassed the new schema policy; 22 archived CodeXGLUE notebooks had nbformat 4.4 cells without raw cell.id fields. Fixed Added a failing archive missing-cell-ID regression, introduced an all-notebook raw schema iterator for S1, promoted archived metadata.id values to raw cell.id, bumped archive notebooks to nbformat_minor: 5, and validated all 51 notebooks with nbformat.validate.
OM-144 High §3.14 tooling / §3.17 notebook trace scripts/rewrite_imports.py, tests/test_rewrite_imports.py The continuation rewrite pass reused protected token positions computed from the original cell after deprecated import lines had been dropped, so continued local bindings such as GraphAttNNParams = \ could be rewritten to NNParams = \ while later local reads stayed unchanged. Fixed Added a failing continued-local-binding regression and recomputed binding protection from the post-import-rewrite line set before the continuation pass.
OM-145 Low §3.6 docs / §3.9 numbered docs docs/architecture.md, mkdocs.yml The architecture page was published under the 2. Architecture MkDocs nav section but its page title and headings still used 1.x numbering, creating a visible nav/page numbering mismatch. Fixed Renumbered the architecture page title to 2. Architecture and normalized its H2 sequence to single-component numbered headings.
OM-146 Low §3.9 numbered docs / §3.13 tests scripts/verify_repo.py, tests/test_verify_repo.py, docs/index.md, docs/architecture.md D9 numbered-heading validation skipped published MkDocs pages docs/index.md and docs/architecture.md, so malformed H2 headings such as 1.1. on H2s were not reported. Fixed Added a failing published-doc D9 regression, included index.md and architecture.md in numbered-doc verification, and normalized the overview and architecture page H2 headings.
OM-147 Medium §3.14 tooling / §3.13 tests scripts/rewrite_imports.py, tests/test_rewrite_imports.py Deprecated Params rewrite binding protection did not treat local class or function definition names as bindings, so after dropping a deprecated import it could rewrite later references to the locally defined GraphAttNNParams or GraphConvNNParams to NNParams. Fixed Added a failing local class/function binding regression and recorded FunctionDef, AsyncFunctionDef, and ClassDef names as protected binding positions in their parent scope.
OM-148 Low §3.9 numbered docs / §3.13 tests scripts/verify_repo.py, tests/test_verify_repo.py, docs/diagrams/README.md D9 published-doc numbered-heading coverage still skipped the published diagram provenance page, so malformed headings in docs/diagrams/README.md could pass verifier checks. Fixed Added a failing diagram provenance D9 regression and included docs/diagrams/README.md in numbered-doc verification.
OM-149 Medium §3.14 tooling / §3.13 tests scripts/rewrite_imports.py, tests/test_rewrite_imports.py Deprecated Params rewrite protection still used module-style first-binding position semantics inside function, lambda, and comprehension scopes, even though Python treats assignments in those scopes as local for the entire scope. Reads before a later local assignment could be rewritten to NNParams, changing local semantics after a deprecated import was dropped. Fixed Added a failing function-local read-before-assignment regression and protected all same-scope deprecated-name references for function, lambda, and comprehension scopes while keeping module/class bodies position-sensitive.
OM-150 Medium §3.17 notebook artifacts / §3.13 tests notebooks/archive/codexglue_summarization/codexglue-summarization-cross-*/notebook.ipynb, tests/nnx_surface/test_notebook_api_surface.py Eight archived CodeXGLUE cross-language notebooks had guarded missing-artifact code but still committed historical BLEU and preview outputs even though their model/bleu_score.test, model/test_0.gold, and model/test_0.output artifacts are not tracked. A clean rerun would show guarded missing-file messages instead. Fixed Added a failing archive output/artifact parity regression, made missing-artifact guard paths display relative archive paths, and refreshed only the eight missing-artifact notebooks' evaluation/preview outputs to the current guard messages; all ten cross-language archive notebooks schema-validate.
OM-151 Low §3.14 tooling / §3.17 runtime trace Makefile, tests/test_makefile_contract.py PYTHON ?= python was configurable and papermill honored it, but setup and asset targets still used ambient pip and python, so make PYTHON=/path/to/python install-torch-stack codespace-setup nlp-assets could install dependencies into a different interpreter than the one later used for notebooks and verification. Fixed Added a failing Makefile dry-run contract test, introduced PIP ?= $(PYTHON) -m pip, and routed setup, NLP asset, and verifier commands through the selected interpreter.