ProgramRepair/.gitignore at main · GLEAM-Lab/ProgramRepair · GitHub

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# Local working state
.codex
now
cache/
data/

# Local manuscript/source working copies
origin_submission/
revised_submission/
diff_submission/
response_letter/
overleaf_latest/
revised_submission_overleaf_*/
artifact/overleaf_after_new_papers_2026-05-01/
artifact/overleaf_before_major_source_2026-05-01/
artifact/revised_submission_base_for_new_paper_diff_2026-05-01/
artifact/frozen_results_2025-10-31/

# Draft manual diffs, patch plans, and local working notes
*_overleaf_*.txt
overleaf_*.txt
*_overleaf_*.patch
manual_diff_*.txt
*_manual_diff_zh_*.txt
major_revision_*.txt
major_revision_*.patch
minimal_localfix_*.txt
minimal_localfix_*.patch
balanced_localfix_*.txt
balanced_localfix_*.patch
localfix_*.txt
localfix_*.patch
strict_remaining_diff_*.txt
review_resolution_audit_*.md
rq_*_diff_*.txt
final_polish_manual_diff_*.txt
final_hygiene_manual_diff_*.txt
fixed_taxonomy_table_*.txt
major_revision.txt
submission_consistency_audit_*.md
remaining_alignment_diff_*.txt
diff.txt
newpic.png

# Annotation handoff scratch files
annotation_followup_20260503/
screening_annotation_template_462_coder1and2.csv
screening_annotation_missing_12_two_coder.csv
human_taxonomy_annotation_1.csv
human_taxonomy_annotation_2.csv
artifact/*_zh.md
artifact/*_zh_*.txt
artifact/screening_annotation_template_462.csv
artifact/screening_reference_labels_462.csv

# Non-public update-sweep and full-text working artifacts
artifact/latest_*
artifact/new_*
artifact/major_revision_*
artifact/fulltext_*
artifact/pipeline_update_sweep_rerun_2026-05-01.md
artifact/published_only_update_decisions_2026-05-01.md
artifact/screening_counts_reproduction_note_zh_2026-05-01.txt
artifact/zotero_update_report_2026-05-01.csv
artifact/人工标注说明_外发版.md
artifact/benchmark_pdf_mentions*.csv
artifact/benchmark_pdf_mentions_summary.md
artifact/benchmark_rq3_*manual_diff_zh_*.txt
artifact/extract_pdf_benchmark_mentions.py
artifact/pdf_text_cache/
artifact/annotation_to_send/
.venv-pdf/
*:Zone.Identifier

# Local remote-run caches
results/
remote_results/cache/
remote_results/data/
remote_results/__pycache__/
remote_results/cdp_command.ps1
remote_results/cdp_eval.ps1
remote_results/download_open_access_pdfs.py
remote_results/update_zotero_major_revision.py

# Local figure drafts not referenced by the public artifact
figure_sources/framework_pipeline*.html
figure_sources/workflow_archetypes.html

# LaTeX build byproducts
*.aux
*.blg
*.log
*.out
*.fdb_latexmk
*.fls
*.synctex.gz