*.bck
*.old
*.swp
*.pyc
__pycache__/
.coverage
.pytest_cache/
build/
dist/
*.egg-info/
bck/
old/
/do_readme.sh

# Local documentation builds and dependencies
docs-site/build/
docs-site/node_modules/

# Generated integration-test artifacts
examples/input/cbicall-test-*.log
examples/input/cbicall-*.yaml
examples/input/cbicall_*/
examples/input/CNAG999_exome/CNAG99901P_ex/cbicall_*/

# Generated report examples and local agent handoff notes
/compare-matrix-demo-runs/
/multiqc_data/
/SESSION*.md
