# Git
.git/
.gitignore
.github/

# Development
.devcontainer/
.vscode/
.serena/
.claude/
.pre-commit-config.yaml
.tox/
.pytest_cache/
.coverage
coverage.xml
htmlcov/

# Build artifacts
build/
dist/
*.egg-info/
__pycache__/
*.pyc
*.pyo

# Documentation
doc/
*.md
*.rst
*.txt
!requirements/*.txt

# Test data (keep test/ for integration tests but exclude large files)
test/*.pdf
test/*.bai
test/build/

# Backup and temp files
*~
*.swp
*.bak
.DS_Store

# Development files
Makefile
PRE-COMMIT-SETUP.md
_notes.txt
bedgraph-plan.txt
changelog-*.txt
commit-log.txt
release-notes-*.md

# Other development directories
play/
devtools/
