# Phase 1 repository cleanup — completion record

## Scope and outcome

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.

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.

## Changes

- 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.

## Exact removals and storage accounting

| Action | Files | Logical bytes |
|---|---:|---:|
| 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 |

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.

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`.

## Verification

| Check | Result |
|---|---|
| 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 |

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.

**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.

## Publication

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.

## Phase 2 proposal — approval required

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.

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.