# Results-Only Packet Report

Date: 2026-06-28

## Summary

Implemented a results-only replication packet in `replication/clean_repo/chatgpt-alignment-replication-clean-repo`. The package now focuses on reproducing empirical tables and figures from de-identified inputs, with manuscript source and paper-compilation tooling removed.

## What Changed

- Removed the nested `paper/` source tree, including TeX, bibliography, PNAS class/style files, and journal abbreviation files.
- Removed paper-build and Overleaf cross-check scripts:
  - `scripts/build_paper.sh`
  - `scripts/crosscheck_overleaf.py`
- Added the shareable de-identified `inputs/` bundle from the older clean distribution:
  - `inputs/analysis_dataset.csv`
  - `inputs/alignment_results_full.json`
  - `inputs/alignment_results_postNov_runs1_openai.json`
  - `inputs/r/merged_df.rds`
  - `inputs/r/wave1_completers.rds`
  - `inputs/r/wave2_completers.rds`
  - `inputs/inputs_metadata.json`
- Renamed the curated empirical workflow:
  - `--paper` -> `--results`
  - `scripts/run_paper_results.sh` -> `scripts/run_results.sh`
  - `scripts/export_paper_tables.py` -> `scripts/export_results_tables.py`
  - `scripts/collect_paper_artifacts.py` -> `scripts/collect_results_artifacts.py`
  - `scripts/prune_paper_outputs.py` -> `scripts/prune_results_outputs.py`
  - `output/paper_tables/` -> `output/results_tables/`
  - `output/paper_artifacts/` -> `output/results_artifacts/`
- Rewrote `README.md` around quick start, curated results, bootstrap smoke/full runs, bundled inputs, optional annotation regeneration, and generated output locations.

## Input Audit

The copied `inputs/` bundle is the de-identified bundle from the prior clean distribution. A spot check found:

- `analysis_dataset.csv`: 1,317 rows and 6 columns: anonymized `rid`, pre/post outcome fields, and MFQ covariates.
- Annotation JSONs: 1,315 rows each, keyed by anonymized `rid`; entries contain numeric foundation/alignment scores and metadata, not transcript text.
- `inputs/r/`: the three RDS files required by `analysis/r/00_main_from_inputs.R`.

No raw private survey exports or transcript files were added. The optional annotation regeneration path still requires a local transcript export under `data/dec_3_2024_wave_1.csv`; that file is not included.

## Verification

Completed:

- `bash -n run_replication.sh scripts/run_results.sh scripts/smoke.sh`
- `./run_replication.sh --help`
- `python3 -m compileall analysis scripts`
- `Rscript` dependency probe for the R pipeline packages
- `RESULTS_ONLY=1 BOOT_REPS=10 N_CORES=1 Rscript analysis/r/00_main_from_inputs.R`
- `BOOT_REPS=10 N_CORES=1 ./run_replication.sh --results --run-r`
- `BOOT_REPS=1000 N_CORES=1 ./run_replication.sh --results --run-r`

The low-rep wrapper smoke completed successfully and emitted the expected low-bootstrap warning. The full wrapper command completed successfully with `BOOT_REPS=1000 N_CORES=1`, producing curated result tables, curated result artifacts, `output/results_artifacts/MANIFEST_SHA256.txt`, and `output/release/chatgpt-alignment-results-artifacts.zip`.

## Truth Claim

What is solved now: the clean package tree has been converted into a results-only replication packet with manuscript source/build/crosscheck surfaces removed, de-identified inputs included, and the curated empirical workflow renamed to results terminology.

What kind of solution this is: implemented fork/package reshaping with full release-command verification.

What remains before public release: final human review of the generated artifact bundle and release/archive mechanics.

Evidence: package inventory contains no TeX/Bib/class/style files and no `paper/` directory; README and scripts expose `--results`; Python syntax checks passed with `python3`; low-rep and full wrapper runs completed from bundled inputs; `output/results_artifacts/MANIFEST_SHA256.txt` and `output/release/chatgpt-alignment-results-artifacts.zip` were generated by the full run.
