| # Phase 1 repository cleanup — completion record |
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| ## Scope and outcome |
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| Implemented the user's approved Phase 1: presentation, navigation, small exact duplicates and future Git LFS tracking. Research execution remains closed. No TEST split, TEST dataset rows or raw TEST predictions were opened; no inference, training, data recomputation or checkpoint migration occurred. |
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| The master evidence report and two original prompts remain byte-identical. Frozen data, results, checkpoint and tooling payloads remain at their original paths. Phase 2 large-artifact deduplication and Phase 3 HF data projection remain unapproved. |
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| ## Changes |
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| - Rebuilt [README](../README.md) around final findings, source-linked metrics, honest limitations, repository navigation and disaster recovery. |
| - Rendered 10 scientific figures in SVG/PNG and one measured C-L1 GIF. [Captions and source paths](../figures/README.md); [input/output SHA-256](../figures/provenance.json); [generator](../scripts/build_publication_assets.py). |
| - Replaced 114 decorative report-wrapper pages with [one historical index](history/README.md). Every original scientific report stays in `results/`. |
| - Archived five obsolete decorative images and linked current documentation to the scientific figure set. Previous figure and documentation bytes remain in the verified preservation archive. |
| - Canonicalized judge-package consumers to `audit/llm_judge/package`. A relative local alias keeps historical root-path callers working without duplicated card payloads. |
| - Preserved the two distinct old judge manifests as real, byte-identical files under `docs/history/legacy_judge_package/`. |
| - Added the [code guide](CODE_GUIDE.md), updated the [documentation index](README.md) and [HF archive guide](HF_ARCHIVE.md), and fixed maintained navigation targets. |
| - Preserved all nine previously uncommitted source/test files. Eight are byte-identical; the analyzer's only approved change is its canonical package path. Original source bytes are backed up. |
| - Added `.gitattributes` aligned with the actual parent Git root. PNG/GIF and durable binary artifacts use LFS for future commits; existing history is not migrated or rewritten. Existing HF attribute rules are retained. |
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| ## Exact removals and storage accounting |
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| | Action | Files | Logical bytes | |
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| | Exact judge payload duplicates removed after canonical re-hash | 152 | 636,382 | |
| | Redundant historical wrapper pages archived, then removed live | 114 | 64,906 | |
| | Obsolete decorative images archived, then removed live | 5 | 31,481 | |
| | Unique judge manifests relocated, not discarded | 2 | 19,081 | |
| | Total superseded live paths | 273 | 751,850 | |
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| The duplicate removal eliminates **636,382 logical bytes** of redundant live payloads. This is a presentation cleanup, not a large storage-reclamation phase. New high-resolution figure exports use 1,411,328 bytes versus 60,473 bytes in the previous root figure collection; preservation archives and new assets add storage. **No claim of net disk savings is made.** Large checkpoint, dataset, environment and archive bytes are untouched. |
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| Every removed live path is listed in the [removal map](../releases/2026-10-12-phase1-cleanup/removal_manifest.json), with a preserved destination/archive member and SHA-256. Original presentation archive: `24f049db7c5bd7379db8b1b3e2958861b6b1d967ad271f920f52d023e6f3f60f`; remotely downloaded and verified before any removals, revision `fd8b4790fcb94d6719a3e7ebca47ab8585354d57`. |
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| ## Verification |
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| | Check | Result | |
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| | Full suite | **552 passed in 32.42 seconds**; two added canonical-path/validation regressions | |
| | Frozen payload metadata | **20,051 checked; zero changed payloads, zero missing files** | |
| | Accepted grading cards | **150** sequential cards; 75 reasoning / 75 no-reasoning; blocklist passes; content/order checked against accepted blinded deck | |
| | Existing grades | **150** records validated against their frozen SHA-256 and dimension rules | |
| | Exact canonical duplicates | **152** hashes match pre-cleanup originals | |
| | Original prompts | Both byte-identical | |
| | Master report | Byte-identical | |
| | Internal imports | **490** edges resolve; no syntax errors | |
| | Figure provenance | Every registered input/output hash verifies | |
| | LFS | PNG/GIF, adapters, state/archive binaries match rules; SVG stays ordinary text; no history migration | |
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| Evidence: layout/integrity/test logs are included in the release bundle. A legacy test refreshes the mtime of `results/phase10/human_audit/blinding_check.json`; its SHA-256 remains unchanged and the side effect is recorded. |
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| **Historical reference exception:** the original literature-review prompt contains five image links to assets never supplied with it. Their absence is explained in [the prompt index](prompts/README.md). Original prompt bytes are preserved; no replacement experimental evidence is invented. These are not counted as working current navigation links. Historical raw reports also retain their original text. |
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| ## Publication |
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| The cleaned browsing view, all original/replaced presentation bytes, changed source and verification records are published under private HF `Dhruv1000/tracegrpo`. [Release index](../releases/2026-10-12-phase1-cleanup/README.md) describes payload manifests and the machine-readable remote verification status. Existing large bundles are retained without re-upload. |
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| ## Phase 2 proposal — approval required |
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| Review the 228 verified duplicate hash groups individually, beginning with repeated immutable tokenizer files and identical adapter payloads. Before consolidating a checkpoint, verify optimizer/scheduler/RNG and step provenance as well as weights. Preserve every expected load/restore path; test aliases or hardlinks before applying them. No dataset, unique checkpoint state, result, interrupted-run evidence or recovery archive is removed. No Git history pruning, new experiments or TEST reads. |
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| The audit's approximately 1.56 GB repeated-byte estimate is an upper-bound candidate inventory, not guaranteed reclaimable storage. Proceed only after explicit user approval of Phase 2's exact file-level plan. |
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