chore(repo): initialize reproducible research workspace
This commit is contained in:
Jinotech
@@ -0,0 +1,671 @@
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# Errors
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Command failures and integration errors.
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---
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## [ERR-20260920-006] powershell-empty-pipe
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**Logged**: 2026-09-20
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**Priority**: low
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**Status**: resolved
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**Area**: infra
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### Summary
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A final artifact verification command piped directly from a PowerShell `foreach` statement and produced an empty-pipe parser error.
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### Error
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`ParserError: An empty pipe element is not allowed.`
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### Context
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Read-only existence and size verification for the four Stage 0 deliverables and Progression.md.
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### Suggested Fix
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Collect `foreach` output into an array first, then pipe the array to `Format-Table`.
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### Metadata
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- Reproducible: yes
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- Related Files: `Progression.md`
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- Pattern-Key: shell.nonzero-exit
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### Resolution
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- **Resolved**: 2026-09-20
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- **Notes**: The corrected command verified all required deliverables exist and contain data.
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---
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## [ERR-20260920-004] progression-patch-context
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**Logged**: 2026-09-20
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**Priority**: low
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**Status**: resolved
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**Area**: docs
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### Summary
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A combined large patch failed because one Progression.md context line did not match byte-for-byte.
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### Error
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`apply_patch verification failed: Failed to find expected lines`
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### Context
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Attempted to create the project charter and update multiple distant sections of the progress archive in one patch.
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### Suggested Fix
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Split artifact creation from progress updates and use smaller, exact context anchors confirmed with `rg`.
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### Metadata
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- Reproducible: unknown
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- Related Files: `Progression.md`, `research/protocol/project_charter.md`
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- Pattern-Key: config.patch-context-mismatch
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### Resolution
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- **Resolved**: 2026-09-20
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- **Notes**: Re-read the mandatory context and split the operation into smaller patches.
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- **Recurrence-Count**: 2
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- **Last-Seen**: 2026-09-20
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---
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## [ERR-20260920-005] spreadsheet-marker-path
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**Logged**: 2026-09-20
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**Priority**: low
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**Status**: resolved
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**Area**: infra
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### Summary
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The spreadsheet skill's operation marker was not located at the dependency-root path shown by the generic example.
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### Error
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`Cannot find module ...dependencies\\container_tools\\mark_artifact_operation_started.mjs`
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### Context
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Preparing to author the literature matrix with the bundled artifact runtime.
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### Suggested Fix
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Resolve the marker from the installed spreadsheet skill directory rather than the dependency root.
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### Metadata
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- Reproducible: yes
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- Related Files: `research/protocol/literature_matrix.xlsx`
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- Pattern-Key: config.missing-script
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### Resolution
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- **Resolved**: 2026-09-20
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- **Notes**: Located the marker under the versioned spreadsheet skill and ran it successfully before authoring.
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---
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## [ERR-20260920-002] restricted-system-inventory
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**Logged**: 2026-09-20
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**Priority**: low
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**Status**: resolved
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**Area**: infra
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### Summary
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WMI, `Get-Volume`, and `systeminfo` returned access denied during the environment audit.
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### Error
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`Access denied` / `拒绝访问`
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### Context
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Attempted read-only OS, RAM, and volume inventory inside the managed Windows execution environment.
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### Suggested Fix
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Use unprivileged fallbacks: .NET runtime information, `Microsoft.VisualBasic.Devices.ComputerInfo`, and `Get-PSDrive`.
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### Metadata
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- Reproducible: yes
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- Related Files: `research/audit/environment_audit.md`
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- Pattern-Key: fs.permission-denied
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### Resolution
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- **Resolved**: 2026-09-20
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- **Notes**: Fallback interfaces returned OS architecture, physical RAM, and filesystem free space without escalation.
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---
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## [ERR-20260920-003] python-package-detection
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**Logged**: 2026-09-20
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**Priority**: low
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**Status**: resolved
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**Area**: infra
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### Summary
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The first package audit used import names derived mechanically from distribution names and produced unreliable missing-package results; a follow-up also attempted to import absent `psutil`.
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### Error
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`ModuleNotFoundError: No module named 'psutil'`
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### Context
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Auditing the local Python scientific stack. Distribution names such as `scikit-learn` do not map mechanically to import names.
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### Suggested Fix
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Query installed distribution versions directly with `importlib.metadata.version()` and handle `PackageNotFoundError` without importing packages.
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### Metadata
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- Reproducible: yes
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- Related Files: `research/audit/environment_audit.md`
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- Pattern-Key: deps.module-not-found
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### Resolution
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- **Resolved**: 2026-09-20
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- **Notes**: The final package table was generated directly from distribution metadata; hardware memory used a .NET fallback.
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---
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## [ERR-20260920-001] pdf-to-markdown-encoding
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**Logged**: 2026-09-20
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**Priority**: medium
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**Status**: resolved
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**Area**: docs
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### Summary
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PDF text extraction failed because Python wrote a Unicode character that could not be encoded using the Windows default code page.
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### Error
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`UnicodeEncodeError: 'gbk' codec can't encode character`
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### Context
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Attempted to extract text from `Document/项目的正式定位.pdf` before passing it through Pandoc.
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### Suggested Fix
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Force UTF-8 output with `PYTHONIOENCODING=utf-8`.
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### Metadata
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- Reproducible: yes
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- Pattern-Key: shell.encoding-error
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---
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## [ERR-20260920-007] winget-access-denied
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**Logged**: 2026-09-20
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**Priority**: medium
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**Status**: pending
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**Area**: infra
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### Summary
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The Windows Package Manager launcher exists but cannot be executed from the managed environment.
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### Error
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`Program 'winget.exe' failed to run: 系统无法访问此文件。`
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### Context
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Attempted to inventory/install R, Python, and CUDA Toolkit through the standard Windows package manager after the user authorized environment remediation.
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### Suggested Fix
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Use vendor-provided official installers, or retry `winget` outside the restricted environment if explicit escalation makes the launcher accessible.
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### Metadata
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- Reproducible: yes
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- Related Files: `Progression.md`, `research/audit/environment_audit.md`
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- Pattern-Key: tool.access-denied
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---
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## [ERR-20260920-008] uv-python-patch-path
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**Logged**: 2026-09-20
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**Priority**: low
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**Status**: resolved
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**Area**: infra
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### Summary
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The virtual-environment command hard-coded a Python 3.12 patch-version path that differed from the version resolved by `uv`.
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### Error
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`No interpreter found at path .python\\cpython-3.12.11-windows-x86_64-none\\python.exe`
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### Context
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`uv python install 3.12` correctly resolved CPython 3.12.14, while the following command assumed 3.12.11.
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### Suggested Fix
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Resolve the installed interpreter path from `uv python find` or enumerate the installation directory rather than hard-coding a patch version.
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### Metadata
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- Reproducible: yes
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- Related Files: `Progression.md`
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- Pattern-Key: config.version-path-mismatch
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### Resolution
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- **Resolved**: 2026-09-20
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- **Notes**: Located `E:\\Model\\.python\\cpython-3.12.14-windows-x86_64-none\\python.exe`; subsequent environment creation will use this exact path.
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---
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## [ERR-20260920-009] research-env-smoke-failures
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**Logged**: 2026-09-20
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**Priority**: high
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**Status**: pending
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**Area**: infra
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### Summary
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The first research-environment runtime test found cache-permission, package-API, and CPU-only PyTorch problems despite a clean dependency-metadata check.
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### Error
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`PermissionError` for PyTensor/Matplotlib/skrub cache paths; `TypeError: check_array() got an unexpected keyword argument 'force_all_finite'`; `torch.cuda.is_available() is false`.
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### Context
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Executed PyMC sampling, semopy CFA, factor analysis, module imports, and a CUDA matrix multiplication in the new Python 3.12 environment.
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### Suggested Fix
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Redirect all caches into the writable project tree, pin a factor-analyzer-compatible scikit-learn release, and reinstall a matched Torch/TorchVision/TorchAudio set from the official CUDA wheel index.
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### Metadata
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- Reproducible: yes
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- Related Files: `research/environment/smoke_test.py`, `research/environment/smoke-test-result.json`, `Progression.md`
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- Pattern-Key: deps.runtime-compatibility
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### Resolution
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- **Resolved**: 2026-09-20
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- **Notes**: Redirected caches into `E:\\Model\\.cache`, pinned scikit-learn 1.6.1, and installed matched CUDA 13.0 builds of Torch 2.14.0 and TorchVision 0.29.0. Torchaudio was removed because no same-generation official wheel exists and the project has no audio workload. Final closure is supported by the second smoke test recorded in `Progression.md`.
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---
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## [ERR-20260920-010] torchaudio-release-mismatch
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**Logged**: 2026-09-20
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**Priority**: low
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**Status**: resolved
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**Area**: infra
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### Summary
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The requested CUDA 13.0 Torch 2.14 stack could not be resolved because the official index does not publish torchaudio 2.14.0 for Windows/Python 3.12.
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### Error
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`No solution found ... there is no version of torchaudio==2.14.0`.
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### Context
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Attempted to align torch, torchvision, and torchaudio at the Torch 2.14 generation using the official CUDA 13.0 wheel index.
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### Suggested Fix
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Do not install torchaudio when the project has no audio workload; keep only matched torch and torchvision CUDA builds.
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### Metadata
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- Reproducible: yes
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- Related Files: `research/environment/python-requirements.in`, `Progression.md`
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- Pattern-Key: deps.release-mismatch
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### Resolution
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- **Resolved**: 2026-09-20
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- **Notes**: Removed torchaudio from the project requirements and smoke-test contract after verifying the official index.
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---
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## [ERR-20260920-011] r-installer-file-race
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**Logged**: 2026-09-20
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**Priority**: low
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**Status**: resolved
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**Area**: infra
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### Summary
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The silent R installer returned before the first immediate `Rscript` invocation observed the completed target files.
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### Error
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`Rscript.exe is not recognized` immediately after installer return.
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### Context
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Installed R 4.6.1 into the project-local tools directory with the official CRAN Windows installer.
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### Suggested Fix
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After installer return, poll for the expected executable or perform a separate verification step before declaring failure.
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### Metadata
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- Reproducible: unknown
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- Related Files: `Progression.md`
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- Pattern-Key: installer.completion-race
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### Resolution
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- **Resolved**: 2026-09-20
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- **Notes**: A follow-up inventory showed a complete installation; `Rscript` reported R 4.6.1 x64 successfully.
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---
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## [ERR-20260920-012] r-smoke-false-positive
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**Logged**: 2026-09-20
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**Priority**: high
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**Status**: resolved
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**Area**: tests
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### Summary
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The first R smoke test marked the mirt test as passed even though the fitted model reported non-convergence.
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### Error
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The JSON result contained `status: passed` together with `converged: false`.
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### Context
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The test wrapper treated any expression that returned without raising an R error as success; the mirt block returned its optimizer flag but did not assert it.
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### Suggested Fix
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Use data generated from an identifiable 2PL model and raise an explicit error unless `fit@OptimInfo$converged` is true.
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### Metadata
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- Reproducible: yes
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- Related Files: `research/environment/r-smoke-test.R`, `research/environment/r-smoke-test-result.json`, `Progression.md`
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- Pattern-Key: tests.missing-assertion
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### Resolution
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- **Resolved**: 2026-09-20
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- **Notes**: Added an explicit convergence assertion, identifiable 2PL simulation, and a higher EM-cycle ceiling. A second run is required for environmental acceptance.
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---
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## [ERR-20260920-013] tool-poll-key-escaping
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**Logged**: 2026-09-20
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**Priority**: low
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**Status**: resolved
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**Area**: infra
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### Summary
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Two CUDA installer status polls failed because a hyphenated nested-tool argument key was not quoted in JavaScript.
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### Error
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`SyntaxError: Unexpected string` / `SyntaxError: Invalid or unexpected token`.
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### Context
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Polling an already-running installer session; the failed polls did not send input or alter the installer process.
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### Suggested Fix
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Quote hyphenated object keys, e.g. `{"yield-time_ms": 30000}`.
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### Metadata
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- Reproducible: yes
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- Related Files: `Progression.md`
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- Pattern-Key: tooling.javascript-object-key
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### Resolution
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- **Resolved**: 2026-09-20
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- **Notes**: Corrected the key quoting and continued polling the same session until the installer returned exit code 0.
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---
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## [ERR-20260920-014] vsdevcmd-nested-quoting
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**Logged**: 2026-09-20
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**Priority**: low
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**Status**: resolved
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**Area**: infra
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### Summary
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The first CUDA compile command failed before invoking the compiler because nested `cmd.exe` quoting truncated the Visual Studio path at the first space.
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### Error
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`'""C:\\Program' is not recognized as an internal or external command`.
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### Context
|
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Attempted to chain `VsDevCmd.bat`, nvcc, and the smoke executable in a single quoted `cmd.exe /c` string.
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### Suggested Fix
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Capture the environment emitted by `VsDevCmd.bat && set`, import it into the PowerShell process, then invoke nvcc directly with argument boundaries managed by PowerShell.
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### Metadata
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- Reproducible: yes
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- Related Files: `research/environment/cuda-smoke.cu`, `Progression.md`
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- Pattern-Key: shell.windows-nested-quoting
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### Resolution
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||||
- **Resolved**: 2026-09-20
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||||
- **Notes**: Switched to importing the Visual Studio environment before compiler invocation; the corrected compile is recorded separately in `Progression.md`.
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---
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## [ERR-20260920-015] nvcc-host-compiler-path
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**Logged**: 2026-09-20
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**Priority**: medium
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**Status**: resolved
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**Area**: infra
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### Summary
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nvcc could not find `cl.exe` after Visual Studio environment variables were copied from a child cmd process into PowerShell.
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### Error
|
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`nvcc fatal: Cannot find compiler 'cl.exe' in PATH`.
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### Context
|
||||
The MSVC component and compiler file were installed, but cross-shell environment import was insufficient for nvcc host-tool discovery.
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||||
### Suggested Fix
|
||||
Run `vcvars64.bat`, nvcc, and the resulting binary inside one cmd process using a checked-in build script.
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||||
|
||||
### Metadata
|
||||
- Reproducible: yes
|
||||
- Related Files: `research/environment/cuda-smoke-build.cmd`, `research/environment/cuda-smoke.cu`, `Progression.md`
|
||||
- Pattern-Key: toolchain.environment-propagation
|
||||
|
||||
### Resolution
|
||||
- **Resolved**: 2026-09-20
|
||||
- **Notes**: Created a single-shell build script after verifying the exact MSVC 14.44 compiler path with vswhere.
|
||||
|
||||
---
|
||||
## [ERR-20260920-016] lock-cache-permissions
|
||||
|
||||
**Logged**: 2026-09-20
|
||||
**Priority**: medium
|
||||
**Status**: resolved
|
||||
**Area**: infra
|
||||
|
||||
### Summary
|
||||
Python and R lock export failed because uv and renv attempted to initialize caches under restricted user-profile directories.
|
||||
|
||||
### Error
|
||||
`Failed to initialize cache ... uv\\cache` and `failed to create directory ... R/cache/R/renv`.
|
||||
|
||||
### Context
|
||||
The runtime caches had been redirected, but the package-manager-specific cache variables were not yet included.
|
||||
|
||||
### Suggested Fix
|
||||
Set `UV_CACHE_DIR` and `RENV_PATHS_ROOT` to writable project-local directories for both activation and export commands.
|
||||
|
||||
### Metadata
|
||||
- Reproducible: yes
|
||||
- Related Files: `research/environment/activate-research.ps1`, `Progression.md`
|
||||
- Pattern-Key: fs.package-manager-cache-permission
|
||||
|
||||
### Resolution
|
||||
- **Resolved**: 2026-09-20
|
||||
- **Notes**: Added project-local uv and renv cache roots; lock export is retried as a separate audited action.
|
||||
|
||||
---
|
||||
## [ERR-20260920-017] r-lock-export-schema
|
||||
|
||||
**Logged**: 2026-09-20
|
||||
**Priority**: medium
|
||||
**Status**: resolved
|
||||
**Area**: infra
|
||||
|
||||
### Summary
|
||||
The R lock snapshot was written, but the auxiliary installed-package export failed due to an assumed metadata column and an incomplete library search path.
|
||||
|
||||
### Error
|
||||
`subscript out of bounds` for the `Repository` column; renv warned that R-recommended packages were missing.
|
||||
|
||||
### Context
|
||||
The export indexed a fixed column list from `installed.packages(lib.loc=project_library)` and passed only the project library to renv.
|
||||
|
||||
### Suggested Fix
|
||||
Combine the project library with `.Library`, and select only metadata columns that actually exist before writing CSV.
|
||||
|
||||
### Metadata
|
||||
- Reproducible: yes
|
||||
- Related Files: `research/environment/renv.lock`, `Progression.md`
|
||||
- Pattern-Key: data.schema-assumption
|
||||
|
||||
### Resolution
|
||||
- **Resolved**: 2026-09-20
|
||||
- **Notes**: The corrected export uses both library roots and intersects requested fields with returned column names; final verification is a separate action.
|
||||
|
||||
---
|
||||
## [ERR-20260920-018] apply-patch-same-file-multiple-operations
|
||||
|
||||
**Logged**: 2026-09-20
|
||||
**Priority**: low
|
||||
**Status**: resolved
|
||||
**Area**: docs
|
||||
|
||||
### Summary
|
||||
A patch attempted to delete and add the same audit file in one invocation and was rejected before making changes.
|
||||
|
||||
### Error
|
||||
`multiple operations target ... environment_audit.md`.
|
||||
|
||||
### Context
|
||||
Replacing the completed environment audit while also adding usage documentation and updating progression state.
|
||||
|
||||
### Suggested Fix
|
||||
Split full-file replacement into separate delete and add operations, then patch other files separately.
|
||||
|
||||
### Metadata
|
||||
- Reproducible: yes
|
||||
- Related Files: `research/audit/environment_audit.md`, `Progression.md`
|
||||
- Pattern-Key: tooling.patch-operation-conflict
|
||||
|
||||
### Resolution
|
||||
- **Resolved**: 2026-09-20
|
||||
- **Notes**: No file changed in the rejected patch; the replacement is retried in valid discrete operations.
|
||||
|
||||
---
|
||||
## [ERR-20260920-019] apply-patch-hunk-order
|
||||
|
||||
**Logged**: 2026-09-20
|
||||
**Priority**: low
|
||||
**Status**: resolved
|
||||
**Area**: docs
|
||||
|
||||
### Summary
|
||||
A combined README/progression patch was rejected because two progression hunks were ordered opposite to their line order in the file.
|
||||
|
||||
### Error
|
||||
`Failed to find expected lines in Progression.md` even though the lines existed.
|
||||
|
||||
### Context
|
||||
One hunk targeted a later risk-table line before another hunk targeted an earlier confirmed-facts line.
|
||||
|
||||
### Suggested Fix
|
||||
Order update hunks from top to bottom within each file, or split unrelated file additions and updates.
|
||||
|
||||
### Metadata
|
||||
- Reproducible: yes
|
||||
- Related Files: `research/environment/README.md`, `Progression.md`
|
||||
- Pattern-Key: tooling.patch-hunk-order
|
||||
|
||||
### Resolution
|
||||
- **Resolved**: 2026-09-20
|
||||
- **Notes**: Added the README separately and applied progression hunks in file order.
|
||||
|
||||
---
|
||||
## [ERR-20260920-020] git-dubious-ownership
|
||||
|
||||
**Logged**: 2026-09-20
|
||||
**Priority**: medium
|
||||
**Status**: resolved
|
||||
**Area**: infra
|
||||
|
||||
### Summary
|
||||
Git refused repository status checks after initialization because the workspace owner differs from the managed execution account.
|
||||
|
||||
### Error
|
||||
`fatal: detected dubious ownership in repository at 'E:/Model'`.
|
||||
|
||||
### Context
|
||||
The repository directory is owned by the Windows Administrators group while commands run as CodexSandboxOffline.
|
||||
|
||||
### Suggested Fix
|
||||
Add only the exact repository path to Git's global `safe.directory`; do not use a wildcard.
|
||||
|
||||
### Metadata
|
||||
- Reproducible: yes
|
||||
- Related Files: `.git`, `Progression.md`
|
||||
- Pattern-Key: git.safe-directory
|
||||
|
||||
### Resolution
|
||||
- **Resolved**: 2026-09-20
|
||||
- **Notes**: The exact-path exception is applied as the next audited action before staging.
|
||||
|
||||
---
|
||||
## [ERR-20260920-021] git-candidate-node-modules
|
||||
|
||||
**Logged**: 2026-09-20
|
||||
**Priority**: medium
|
||||
**Status**: resolved
|
||||
**Area**: infra
|
||||
|
||||
### Summary
|
||||
The first Git candidate set unintentionally included a nested `node_modules` tree, expanding the proposed commit to 7,832 files and about 321 MiB.
|
||||
|
||||
### Error
|
||||
Candidate-size audit showed large native modules and generated JavaScript under `research/experiments/node_modules`.
|
||||
|
||||
### Context
|
||||
The initial `.gitignore` covered research runtimes and caches but omitted generic nested Node dependencies.
|
||||
|
||||
### Suggested Fix
|
||||
Add `**/node_modules/` before staging and rerun the size audit.
|
||||
|
||||
### Metadata
|
||||
- Reproducible: yes
|
||||
- Related Files: `.gitignore`, `Progression.md`
|
||||
- Pattern-Key: git.generated-dependency-tree
|
||||
|
||||
### Resolution
|
||||
- **Resolved**: 2026-09-20
|
||||
- **Notes**: Added the nested dependency ignore rule before any files were staged.
|
||||
|
||||
---
|
||||
## [ERR-20260920-022] git-index-lock-permission
|
||||
|
||||
**Logged**: 2026-09-20
|
||||
**Priority**: medium
|
||||
**Status**: resolved
|
||||
**Area**: infra
|
||||
|
||||
### Summary
|
||||
The first staging attempt could read the repository but could not create `.git/index.lock` under the managed filesystem profile.
|
||||
|
||||
### Error
|
||||
`fatal: Unable to create 'E:/Model/.git/index.lock': Permission denied`.
|
||||
|
||||
### Context
|
||||
The workspace is writable, while repository metadata is protected and requires the authorized elevated Git operation path.
|
||||
|
||||
### Suggested Fix
|
||||
Retry only the required Git index/commit operations with escalation; do not change workspace ownership or weaken filesystem permissions.
|
||||
|
||||
### Metadata
|
||||
- Reproducible: yes
|
||||
- Related Files: `.git`, `Progression.md`
|
||||
- Pattern-Key: git.index-lock-permission
|
||||
|
||||
### Resolution
|
||||
- **Resolved**: 2026-09-20
|
||||
- **Notes**: No files were staged in the failed attempt; the audited candidate set is retried with scoped Git authorization.
|
||||
|
||||
---
|
||||
## [ERR-20260920-023] git-null-excludesfile
|
||||
|
||||
**Logged**: 2026-09-20
|
||||
**Priority**: low
|
||||
**Status**: resolved
|
||||
**Area**: infra
|
||||
|
||||
### Summary
|
||||
Git for Windows rejected `NUL` as an explicit global excludes file override.
|
||||
|
||||
### Error
|
||||
`fatal: cannot use NUL as an exclude file`.
|
||||
|
||||
### Context
|
||||
The override was intended only to silence warnings from an unreadable user-level ignore file; project ignore rules were already valid.
|
||||
|
||||
### Suggested Fix
|
||||
Remove the override and tolerate the harmless warning, or use an actual readable empty file if silence is necessary.
|
||||
|
||||
### Metadata
|
||||
- Reproducible: yes
|
||||
- Related Files: `.gitignore`, `Progression.md`
|
||||
- Pattern-Key: git.excludesfile-windows-device
|
||||
|
||||
### Resolution
|
||||
- **Resolved**: 2026-09-20
|
||||
- **Notes**: The override is removed; no index changes occurred in the failed attempt.
|
||||
|
||||
---
|
||||
@@ -0,0 +1,5 @@
|
||||
# Feature Requests
|
||||
|
||||
Capabilities requested by the user.
|
||||
|
||||
---
|
||||
@@ -0,0 +1,5 @@
|
||||
# Learnings
|
||||
|
||||
Corrections, insights, and knowledge gaps captured during development.
|
||||
|
||||
---
|
||||
Reference in New Issue
Block a user