Add repo-wide duplicate file content audit without cleanup - PR 10.26

# CODEX COMMANDS

model: gpt-5.3-codex
reasoning: medium

Apply PR_10_26_REPO_DUPLICATE_FILE_CONTENT_AUDIT.

Required:
- Add a repo-wide duplicate file content audit.
- Scan by exact content hash.
- Exclude noisy folders: .git, node_modules, tmp, dist, build, coverage, .cache, .next.
- Generate JSON report at docs/dev/reports/repo_duplicate_file_content_audit.json.
- Generate markdown report at docs/dev/reports/PR_10_26_REPO_DUPLICATE_FILE_CONTENT_AUDIT_report.md.
- Include classifications and cleanup risk.
- Do not delete, move, or rewrite duplicate files in this PR.
- Do not modify start_of_day folders.
- Return ZIP artifact at tmp/PR_10_26_REPO_DUPLICATE_FILE_CONTENT_AUDIT_delta.zip.

Classify duplicate file content and safely clean only confirmed duplicate SSoT copies - PR 10.27

Author: DavidQ

docs/dev/codex_commands.md

@@ -1,15 +1,16 @@
 # CODEX COMMANDS
 
 model: gpt-5.3-codex
-reasoning: low
+reasoning: medium
 
-Apply PR_10_25_SAMPLE_METADATA_SSOT_DUPLICATE_EVIDENCE_FIX.
+Apply PR_10_27_DUPLICATE_CLASSIFICATION_AND_SAFE_CLEANUP.
 
-- Preserve samples/metadata/samples.index.metadata.json as the only live SSoT.
-- Remove, move, or clearly demote the duplicate report evidence copy.
-- Do not keep a repo-relative duplicate that looks like runtime source.
-- Confirm runtime/tool code references only the live SSoT.
-- Do not rewrite sample metadata content.
+Required:
+- Read docs/dev/reports/repo_duplicate_file_content_audit.json from PR 10.26.
+- Classify duplicate groups before cleanup.
+- Remove/demote only confirmed duplicate SSoT or accidental-copy files.
+- Do not delete templates, sample variants, generated reports, validation outputs, or ambiguous groups.
+- Leave ambiguous groups documented with no action.
+- Add report at docs/dev/reports/PR_10_27_DUPLICATE_CLASSIFICATION_AND_SAFE_CLEANUP_report.md.
 - Do not modify start_of_day folders.
-- Add validation report.
-- Return ZIP artifact at tmp/PR_10_25_SAMPLE_METADATA_SSOT_DUPLICATE_EVIDENCE_FIX_delta.zip.
+- Return ZIP artifact at tmp/PR_10_27_DUPLICATE_CLASSIFICATION_AND_SAFE_CLEANUP_delta.zip.

docs/dev/commit_comment.txt

@@ -1 +1 @@
-Remove duplicate sample index metadata evidence copy and preserve samples metadata as SSoT - PR 10.25
+Classify duplicate file content and safely clean only confirmed duplicate SSoT copies - PR 10.27

docs/dev/reports/PR_10_26_REPO_DUPLICATE_FILE_CONTENT_AUDIT_report.md

@@ -0,0 +1,61 @@
+# PR_10_26_REPO_DUPLICATE_FILE_CONTENT_AUDIT Report
+
+## Result
+PASS
+
+## Scope
+- Repo-wide duplicate content audit by exact SHA-256 hash.
+- No duplicate files were deleted, moved, or rewritten in this PR.
+
+## Scan Configuration
+- Excluded directories: .git, node_modules, tmp, dist, build, coverage, .cache, .next
+- Scanned files: 5038
+
+## Summary
+- Duplicate groups: 41
+- Duplicate files (in groups): 138
+- Duplicate content bytes: 390107 (380.96 KB)
+- Potential cleanup savings (extra copies only): 199957 (195.27 KB)
+
+## Classification And Cleanup Risk
+| Classification | Cleanup Risk | Groups | Files | Potential Savings |
+|---|---|---:|---:|---:|
+| runtime-or-source-duplicate | high | 27 | 109 | 125830 (122.88 KB) |
+| report-evidence-snapshot-duplicate | low | 2 | 4 | 38864 (37.95 KB) |
+| runtime-json-duplicate | high | 8 | 17 | 26807 (26.18 KB) |
+| general-content-duplicate | medium | 1 | 2 | 7574 (7.40 KB) |
+| report-artifact-duplicate | low | 2 | 4 | 681 (681 B) |
+| documentation-duplicate | medium | 1 | 2 | 201 (201 B) |
+
+## Top Duplicate Groups By Potential Savings
+| Hash (short) | Count | File Size | Potential Savings | Classification | Risk | Representative File |
+|---|---:|---:|---:|---|---|---|
+| 6a0693de2150 | 2 | 97287 | 97287 | runtime-or-source-duplicate | high | docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative/src/engine/paletteList.js |
+| ef64cc68f2b5 | 2 | 36486 | 36486 | report-evidence-snapshot-duplicate | low | docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative/docs/dev/reports/level_10_6d_palette_contract_evidence/test_sample_standalone_data_flow_output.txt |
+| 4aec342e6ea9 | 2 | 21840 | 21840 | runtime-json-duplicate | high | samples/phase-02/0207/sample.0207.sprite-editor.json |
+| 971437553d34 | 2 | 7574 | 7574 | general-content-duplicate | medium | docs/design/gdd/Capcom/Final Fight/gdd.txt |
+| 84e9d7f94ad1 | 2 | 4456 | 4456 | runtime-or-source-duplicate | high | docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative/tools/shared/paletteDocumentContract.js |
+| 162cc270514e | 7 | 658 | 3948 | runtime-or-source-duplicate | high | samples/phase-01/0101/index.js |
+| e3faab082770 | 2 | 2378 | 2378 | report-evidence-snapshot-duplicate | low | docs/dev/reports/level_10_6d_palette_contract_evidence/palette_shape_diff.json |
+| 937cb7d3e5c7 | 5 | 549 | 2196 | runtime-or-source-duplicate | high | samples/phase-04/0408/index.js |
+| e473e39904ce | 5 | 450 | 1800 | runtime-or-source-duplicate | high | samples/phase-09/0902/index.js |
+| 982e2b63afb7 | 2 | 1430 | 1430 | runtime-or-source-duplicate | high | samples/phase-12/1217/assets/data/vector/mario_style_learning_backdrop.svg |
+| 167733ac880e | 2 | 1341 | 1341 | runtime-json-duplicate | high | docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative/samples/phase-02/0213/sample.0213.palette.json |
+| 7c3809e1621e | 2 | 1279 | 1279 | runtime-or-source-duplicate | high | samples/phase-12/1220/assets/data/parallax/mario_style_bushes_foreground.svg |
+| 90b443049931 | 2 | 1225 | 1225 | runtime-json-duplicate | high | docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative/tools/schemas/palette.schema.json |
+| 257ace0d8424 | 2 | 1208 | 1208 | runtime-or-source-duplicate | high | samples/phase-12/1220/assets/data/parallax/mario_style_clouds.svg |
+| e76f7162ba07 | 3 | 585 | 1170 | runtime-or-source-duplicate | high | samples/phase-12/1218/assets/data/parallax/hero-proxy.svg |
+| 2df11510e899 | 2 | 1081 | 1081 | runtime-or-source-duplicate | high | samples/phase-12/1218/assets/data/parallax/foreground-occluder.svg |
+| ceb6a130e4bc | 2 | 1053 | 1053 | runtime-or-source-duplicate | high | samples/phase-12/1218/assets/data/parallax/cloud-bands.svg |
+| d8022975b2f9 | 2 | 1012 | 1012 | runtime-or-source-duplicate | high | samples/phase-12/1215/assets/data/vector/sky_gradient_scene.svg |
+| 83e6f07dfc44 | 3 | 412 | 824 | runtime-or-source-duplicate | high | samples/phase-12/1218/assets/data/parallax/sky-gradient.svg |
+| 8bdc50fa968a | 2 | 812 | 812 | runtime-or-source-duplicate | high | samples/phase-12/1216/assets/data/vector/mountain_range_scene.svg |
+| 2adef45cfa82 | 4 | 264 | 792 | runtime-or-source-duplicate | high | games/_template/assets/parallax/data/README.md |
+| eaebc2a6b996 | 2 | 659 | 659 | report-artifact-duplicate | low | docs/dev/reports/asset_ownership_strategy_validation.txt |
+| ff7a6cd3249e | 2 | 633 | 633 | runtime-json-duplicate | high | docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative/samples/phase-03/0308/sample.0308.palette.json |
+| 62df597da971 | 2 | 633 | 633 | runtime-json-duplicate | high | docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative/samples/phase-03/0313/sample.0313.palette.json |
+| 3a3c84dde6f2 | 2 | 624 | 624 | runtime-or-source-duplicate | high | samples/phase-12/1220/assets/data/parallax/mario_style_hills.svg |
+
+## Notes
+- Full duplicate group details are in `repo_duplicate_file_content_audit.json`.
+- High-risk groups should be reviewed by code/data owners before any consolidation.

docs/dev/reports/PR_10_27_DUPLICATE_CLASSIFICATION_AND_SAFE_CLEANUP_report.md

@@ -0,0 +1,98 @@
+# PR_10_27_DUPLICATE_CLASSIFICATION_AND_SAFE_CLEANUP Report
+
+## Result
+PASS
+
+## Input
+- Source audit: `docs/dev/reports/repo_duplicate_file_content_audit.json`
+- Duplicate groups reviewed: `41`
+
+## Classification Counts
+| Classification | Groups |
+|---|---:|
+| duplicate-ssot | 0 |
+| accidental-copy | 0 |
+| report-evidence | 9 |
+| generated-validation | 2 |
+| template-intentional | 3 |
+| sample-variant-intentional | 23 |
+| ambiguous-no-action | 4 |
+
+## Safe Cleanup Actions Applied
+- Action performed: demoted runtime-looking report-evidence snapshot files (moved, not deleted).
+- Files moved: `7`
+  - `docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative/samples/phase-02/0213/sample.0213.palette.json` -> `docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative_demoted_runtime_lookalikes/samples/phase-02/0213/sample.0213.palette.json`
+  - `docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative/samples/phase-03/0308/sample.0308.palette.json` -> `docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative_demoted_runtime_lookalikes/samples/phase-03/0308/sample.0308.palette.json`
+  - `docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative/samples/phase-03/0313/sample.0313.palette.json` -> `docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative_demoted_runtime_lookalikes/samples/phase-03/0313/sample.0313.palette.json`
+  - `docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative/src/engine/paletteList.js` -> `docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative_demoted_runtime_lookalikes/src/engine/paletteList.js`
+  - `docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative/tools/schemas/palette.schema.json` -> `docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative_demoted_runtime_lookalikes/tools/schemas/palette.schema.json`
+  - `docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative/tools/schemas/tools/palette-browser.schema.json` -> `docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative_demoted_runtime_lookalikes/tools/schemas/tools/palette-browser.schema.json`
+  - `docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative/tools/shared/paletteDocumentContract.js` -> `docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative_demoted_runtime_lookalikes/tools/shared/paletteDocumentContract.js`
+
+## Files Intentionally Kept
+- All template duplicates (`template-intentional`) were kept unchanged.
+- All sample-variant duplicates (`sample-variant-intentional`) were kept unchanged.
+- All generated report/validation duplicates (`generated-validation`) were kept unchanged.
+- Any unresolved groups were marked `ambiguous-no-action` and left untouched.
+
+## Ambiguous Groups Left Untouched
+| Hash (short) | Representative File | Reason |
+|---|---|---|
+| 971437553d34 | `docs/design/gdd/Capcom/Final Fight/gdd.txt` | Potential intentional/doc-specific duplication or unclear ownership |
+| df859606f030 | `tools/palette-editor/tool.schema.json` | Potential intentional/doc-specific duplication or unclear ownership |
+| f01a374e9c81 | `games/Pacman/assets/.gitkeep` | Potential intentional/doc-specific duplication or unclear ownership |
+| e3b0c44298fc | `docs/design/gdd/Nameco/Galaga/gdd.txt` | Potential intentional/doc-specific duplication or unclear ownership |
+
+## Group-by-Group Classification
+| Hash (short) | Count | Classification | Action | Cleanup Risk | Representative File |
+|---|---:|---|---|---|---|
+| 6a0693de2150 | 2 | report-evidence | demoted-moved | high | `docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative/src/engine/paletteList.js` |
+| ef64cc68f2b5 | 2 | report-evidence | kept-no-action | low | `docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative/docs/dev/reports/level_10_6d_palette_contract_evidence/test_sample_standalone_data_flow_output.txt` |
+| 4aec342e6ea9 | 2 | sample-variant-intentional | kept-no-action | high | `samples/phase-02/0207/sample.0207.sprite-editor.json` |
+| 971437553d34 | 2 | ambiguous-no-action | kept-no-action | medium | `docs/design/gdd/Capcom/Final Fight/gdd.txt` |
+| 84e9d7f94ad1 | 2 | report-evidence | demoted-moved | high | `docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative/tools/shared/paletteDocumentContract.js` |
+| 162cc270514e | 7 | sample-variant-intentional | kept-no-action | high | `samples/phase-01/0101/index.js` |
+| e3faab082770 | 2 | report-evidence | kept-no-action | low | `docs/dev/reports/level_10_6d_palette_contract_evidence/palette_shape_diff.json` |
+| 937cb7d3e5c7 | 5 | sample-variant-intentional | kept-no-action | high | `samples/phase-04/0408/index.js` |
+| e473e39904ce | 5 | sample-variant-intentional | kept-no-action | high | `samples/phase-09/0902/index.js` |
+| 982e2b63afb7 | 2 | sample-variant-intentional | kept-no-action | high | `samples/phase-12/1217/assets/data/vector/mario_style_learning_backdrop.svg` |
+| 167733ac880e | 2 | report-evidence | demoted-moved | high | `docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative/samples/phase-02/0213/sample.0213.palette.json` |
+| 7c3809e1621e | 2 | sample-variant-intentional | kept-no-action | high | `samples/phase-12/1220/assets/data/parallax/mario_style_bushes_foreground.svg` |
+| 90b443049931 | 2 | report-evidence | demoted-moved | high | `docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative/tools/schemas/palette.schema.json` |
+| 257ace0d8424 | 2 | sample-variant-intentional | kept-no-action | high | `samples/phase-12/1220/assets/data/parallax/mario_style_clouds.svg` |
+| e76f7162ba07 | 3 | sample-variant-intentional | kept-no-action | high | `samples/phase-12/1218/assets/data/parallax/hero-proxy.svg` |
+| 2df11510e899 | 2 | sample-variant-intentional | kept-no-action | high | `samples/phase-12/1218/assets/data/parallax/foreground-occluder.svg` |
+| ceb6a130e4bc | 2 | sample-variant-intentional | kept-no-action | high | `samples/phase-12/1218/assets/data/parallax/cloud-bands.svg` |
+| d8022975b2f9 | 2 | sample-variant-intentional | kept-no-action | high | `samples/phase-12/1215/assets/data/vector/sky_gradient_scene.svg` |
+| 83e6f07dfc44 | 3 | sample-variant-intentional | kept-no-action | high | `samples/phase-12/1218/assets/data/parallax/sky-gradient.svg` |
+| 8bdc50fa968a | 2 | sample-variant-intentional | kept-no-action | high | `samples/phase-12/1216/assets/data/vector/mountain_range_scene.svg` |
+| 2adef45cfa82 | 4 | template-intentional | kept-no-action | high | `games/_template/assets/parallax/data/README.md` |
+| eaebc2a6b996 | 2 | generated-validation | kept-no-action | low | `docs/dev/reports/asset_ownership_strategy_validation.txt` |
+| ff7a6cd3249e | 2 | report-evidence | demoted-moved | high | `docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative/samples/phase-03/0308/sample.0308.palette.json` |
+| 62df597da971 | 2 | report-evidence | demoted-moved | high | `docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative/samples/phase-03/0313/sample.0313.palette.json` |
+| 3a3c84dde6f2 | 2 | sample-variant-intentional | kept-no-action | high | `samples/phase-12/1220/assets/data/parallax/mario_style_hills.svg` |
+| 1a90c49b06ad | 2 | sample-variant-intentional | kept-no-action | high | `samples/phase-17/1708/main.js` |
+| 680b3febde11 | 3 | sample-variant-intentional | kept-no-action | high | `samples/phase-12/1218/assets/data/parallax/mountain-ridge-short.svg` |
+| 9feb79a83d78 | 2 | sample-variant-intentional | kept-no-action | high | `samples/phase-12/1220/assets/data/parallax/mario_style_mountains.svg` |
+| cf89bcd9035a | 2 | sample-variant-intentional | kept-no-action | high | `samples/phase-17/1709/main.js` |
+| 2fb3e00d7762 | 3 | sample-variant-intentional | kept-no-action | high | `samples/phase-12/1218/assets/data/parallax/mountain-ridge-tall.svg` |
+| 6435cd00ef69 | 9 | sample-variant-intentional | kept-no-action | high | `games/AITargetDummy/rules/gameFlowRules.js` |
+| 9a97352ae4b6 | 9 | sample-variant-intentional | kept-no-action | high | `games/Pacman/rules/gameFlowRules.js` |
+| df859606f030 | 3 | ambiguous-no-action | kept-no-action | high | `tools/palette-editor/tool.schema.json` |
+| 9454a8b0c6e3 | 2 | sample-variant-intentional | kept-no-action | high | `samples/phase-12/1220/assets/data/parallax/mario_style_sky.svg` |
+| 7fac6c68998c | 2 | report-evidence | demoted-moved | high | `docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative/tools/schemas/tools/palette-browser.schema.json` |
+| 3a6e82fbca11 | 2 | template-intentional | kept-no-action | medium | `docs/operations/dev/templates/CODEX_AUTO_COMMAND.md` |
+| a54340ac4b79 | 2 | template-intentional | kept-no-action | high | `games/vector-arcade-sample/assets/data/tilemaps/template-ui.tileset.json` |
+| f01a374e9c81 | 24 | ambiguous-no-action | kept-no-action | high | `games/Pacman/assets/.gitkeep` |
+| 1a6ff34ec366 | 2 | sample-variant-intentional | kept-no-action | high | `samples/phase-15/1505/assets/images/hero.png` |
+| 29dc1886e7c3 | 2 | generated-validation | kept-no-action | low | `docs/dev/reports/tool_select_population_validation.md` |
+| e3b0c44298fc | 4 | ambiguous-no-action | kept-no-action | high | `docs/design/gdd/Nameco/Galaga/gdd.txt` |
+
+## Validation
+- Confirmed runtime/tool/test code does not reference demoted evidence paths.
+- Confirmed runtime/tool references to sample metadata still point to live SSoT (`samples/metadata/samples.index.metadata.json`).
+
+## Constraints Check
+- No start_of_day folders modified.
+- No template/sample-variant/generated-validation files were deleted or rewritten.
+- No runtime behavior changes introduced.

docs/dev/reports/REPORT_PR_10_27.md

@@ -0,0 +1,9 @@
+# REPORT_PR_10_27_DUPLICATE_CLASSIFICATION_AND_SAFE_CLEANUP
+
+## Summary
+This PR converts the duplicate-content audit into a safe classified cleanup pass.
+
+## Target
+- Remove only confirmed duplicate SSoT/accidental copies.
+- Preserve intentional duplicates and evidence.
+- Document ambiguous duplicate groups for later review.

docs/dev/reports/level_10_6d_palette_contract_evidence/repo_relative_demoted_runtime_lookalikes/README.md

@@ -0,0 +1,6 @@
+# Demoted Runtime-Looking Evidence Snapshot Files
+
+These files were moved from `repo_relative/` because their paths looked like live runtime/source paths
+(for example `src/...`, `tools/...`, `samples/...`) and were flagged by duplicate-content audit.
+
+They remain report evidence only and are not runtime SSoT.