# ── Build artifacts ──
build/
build_cpu/
bin/
*.o
*.so
*.dylib
*.dll

# ── CMake / generated build files ──
CMakeCache.txt
CMakeFiles/
cmake_install.cmake
Makefile
install_manifest.txt
compile_commands.json

# ── Python ──
__pycache__/
*.pyc
*.pyd

# ── Virtual environments ──
.venv/
env/

# ── Editor / IDE / OS ──
.vscode/
.DS_Store
*.swp
*~

# ── GFA inputs (large) ── tiny hand-verified fixtures are force-added back below
*gfa
!tests/fixtures/*.gfa
!tests/fixtures/deconstruct_inversion_fixture.gfa
!tests/fixtures/deconstruct_pansn_ref_fixture.gfa
!tests/fixtures/deconstruct_reverse_path_fixture.gfa

# ── Compressed containers & large datasets ──
example.gfaz
output.gfaz
chrY*
# Root-level scratch (compressed containers / BED / TSV) — tests/fixtures/*.bed
# stay tracked because these are anchored to the repo root only.
/*.gfaz
/*.bed
/*.tsv
data/
test_data/
reference_repo/

# ── Benchmark / eval outputs ──
.cache/
benchmark_results/
extract_benchmark.csv
scripts/eval_results.csv
scripts/Ecoli*

# ── Local scratch / working files (not for the repo) ──
rebuttal.md
review.md
paper_compute_engine/
fix_cc.py
do_refactor.py
do_refactor_pt2.py
revert_ns.py
