# Rust / build
target/
build/
dist/
*.so
*.egg-info/

# Python
__pycache__/
*.pyc
.venv/
.pytest_cache/
pytest-cache-files-*/

# Docs
docs/_render/
site/

# macOS
.DS_Store

# Local scratch / sidecars (not part of the repo)
/alignment.fasta
/alignment.png
/masked.fasta
*.craic.json
*.craic-history.txt

# Benchmark data (downloaded) and result CSVs (generated) - not part of the repo
/BAliBASE_R10.tar.gz
/RV100/
/balibase*.csv
/sim_results.csv
/benchmark_results.csv
/aligned_out/

# generated macOS app bundle (build with scripts/make_app.py)
CRAIC.app/

# Editor / OS sidecars
~$*
.fuse_hidden*

# Manuscript drafts and backups (not part of the released code)
/paper/

