__pycache__/
*.pyc
.venv/
*.egg-info/
.ruff_cache/
.mypy_cache/
.pytest_cache/
node_modules/
.next/
.env
.env.local
.env*.local
*.db
.DS_Store
internal/

# Large data files
data/*.gz
data/*.gtf
data/*.fa
data/*.fai
data/*.csv
data/probes/
data/chromhmm/
data/gnomad/
data/hpa/
data/msigdb/
data/paxdb/
data/reactome/
data/repeatmasker/
data/herv/
data/clocks/
data/encode/
data/gwas/
.vercel
.superpowers/

# Large reference/experiment data
data/tad/
data/hic/
data/wgbs/
data/accessibility/
data/pcawg/
data/replication/
data/insulation/
data/imgt_hla/
data/dinucleotide_index/
InSilicoExperiments/
benchmark/
viewer/.superpowers/
data/downloads/

# Sensitive documents — never commit to public repo
PROVISIONAL_PATENT_DRAFT.md
*.ownership-certificate.pdf

# Internal docs — not for public repo
CLAUDE.md
COMPUTATIONAL_ASSUMPTIONS.md
VALIDATION_REGISTRY.md
.claude/
docs/superpowers/
viewer/docs/superpowers/
.venv-vcp/
