# Third-party raw input: 7.5 GB, operator-owned. Never committed, and never
# pruned by anything in this repo — three of its origins (HMDB, MiMeDB, MASI)
# are browser-only downloads that no script can re-fetch. `make
# check-data-bounds` reports its size and touches nothing.
data/raw/
# In this checkout `data` and `graph` are symlinks into the sibling
# MicrobiomeKG-Data/ folder (raw/, graph/), so the library tree stays
# clean; the two links are local state like everything they point at.
/data
/graph
*.kgl
graph/
# Written by scripts/build.py beside the graph; a pure function of the sources.
ontology.json

docs/_build/
.venv/
__pycache__/
.pytest_cache/
.ruff_cache/
.DS_Store

# The local working system: plans, scratch, the todo index (dev-docs/) and the
# cross-project channel (inbox/). Local state, never committed — each folder's
# own README.md is its layout map, and CLAUDE.md's R4 table names every tier's
# bound and owner. `make check-dev-docs` enforces the size bound.
/dev-docs/
/inbox/

# Agent skill trees are local working state for this checkout, not part of the
# public repository. The local `make gate` still verifies the adapter mirror.
.claude/skills/
.agents/skills/
