.gitignore

/target
**/target/
*.parquet
!test_data/**/*.parquet
.mumdia_work/
out/
# machine-specific local cargo config (target-dir redirect); see .cargo/config.toml.example
rust/mumdia/.cargo/config.toml

# --- deployment hygiene (Phase 0 cleanup): run outputs, envs, scratch ---
# Python environments + caches
.venv/
__pycache__/
*.pyc
# run-output / data directories (large; not source) and vendor input data
out_*/
mzml_files/
fasta/
sidecar_work/
# build + run logs
*.log
# ad-hoc analysis notebooks, dev notes, scratch configs (not shipped)
notebooks/
/MISS_ANALYSIS*.md
/fragindex_*.md
/*_plan.md
/speedup.md
/cfg_*.json
/config_*.json
/config.aif-*.json
/config.hye-*.json
/-covr2.gitignore
# coverage-instrumented source scratch
*-covr2.rs

# session/experiment drivers + probes (throwaway; hardcoded paths)
scripts/run_*.sh
scripts/_probe*.py

# Root-level research/spec/analysis notes stay local. The public README,
# CLAUDE agent guide, and the tracked docs/ developer guide are source.
/*.md
!/README.md
!/CLAUDE.md
!/CHANGELOG.md
!/CONTRIBUTING.md
!/SECURITY.md
!/CODE_OF_CONDUCT.md
!/THIRD_PARTY_LICENSES.md
# local archive of superseded working docs (not published)
/_archive/
# Emitted by ci/smoke.sh for the cross-platform comparison in CI.
/smoke_output_hashes.txt
# Local benchmark inputs and scratch outputs (tens of GB; never source). The
# imported spectral libraries under lib/ are irreplaceable local data, not build
# output: ignoring them keeps them out of commits without risking deletion.
/lib/
/lib_capped/
/raw_files/
/val*/
/mbr_k3/
/mbr_work/
/missed_xics*/
# Vendored third-party source read for comparison only; not ours to redistribute.
/alphadia/

# Collaborator-specific configs and deployment notes stay local.
# (`/*.md` above already keeps root-level notes local; these cover the configs.)
config.strasbourg*.json
config.*-local.json
# Superseded by configs/examples/*.json, which resolve interpreters with "auto".
# Kept ignored so an existing local copy keeps working without being committed.
config.local-*.json
deploy_local/

# stopgate
.stopgate/state/
.stopgate/log.jsonl
.stopgate/loop.jsonl
.stopgate/bench.json
.stopgate/tmp/
# The rest of the harness's local state. Enumerated like the lines above rather than
# ignoring `.stopgate/` wholesale, so a file the harness starts tracking on purpose is a
# deliberate addition. `handoff.md` was swept into a commit by a `git add -A` before this.
.stopgate/handoff.md
.stopgate/state/
.claude/settings.local.json
.stopgate.toml