.gitignore

nodejs/node_modules/
.vscode/
.llm_cache/

# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

# C extensions
*.so

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/    
lib64/
parts/
sdist/
var/
wheels/
pip-wheel-metadata/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# PyInstaller
*.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
*.log
hs_err_pid*.log
.pytest_cache/
.hypothesis/

# Translations
*.mo
*.pot

# Django stuff:
*.log
local_settings.py
db.sqlite3
db.sqlite3-journal

# Flask stuff:
instance/
.webassets-cache

# Scrapy stuff:
.scrapy

# Sphinx documentation
docs/_build/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# Environments
.env
.env.*
*.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

# uv
uv.lock
venv_community_test/
venv_pyodbc_test/
venv_specific_wheel_test/

# Docker
docker-compose.override.yml
docker-compose.yml.override

# IRIS specific runtime data / large files
iris_container_data/
iris_data_odbc_test/
temp_pmc_download/
data/pmc_oas_downloaded/

# Downloaded archives/installers
*.tar.gz
*.zip
*.whl 
ODBCinstall

# OS-generated files
.DS_Store
.DS_Store?
._*
.Spotlight-V100
.Trashes
ehthumbs.db
Thumbs.db

# IDE / Editor specific
.vscode/
.idea/
*.swp
*~
*.bak

# Investigation and experimental directories
investigation/
scripts_to_review/
debug_archive/
archive/

# Additional temporary files and patterns
*_comparison_*.json
*_chunking_*.json
explore_*.py
research_*.py
test_*_integration.py

# Workspace files
*.code-workspace

# IRIS configuration files
*.cpf
iris.key

# Active ingestion data
ingestion_checkpoint.pkl
data/pmc_100k_downloaded/

temp_iris.key

# Configuration files (.gitignored)
config/

# Output and temporary directories that accumulate files
outputs/logs/
outputs/temp/
test_results/temp/
reports/temp/
comprehensive_ragas_results/temp/
benchmarks/temp/
coverage_html/temp/

# Additional temporary file patterns
*.tmp
*.temp
*.pid
*.lock
*.swp
*~
.mypy_cache/

# Test and evaluation outputs (keep structure but ignore content)
outputs/**/*.log
test_results/**/*.log
reports/**/*.log
evaluation_framework/**/*.log
test-results/
coverage_html/
lint-results/

# Additional cleanup entries (Feature 052)
logs/
tests/artifacts/
coverage.json

# Development tracking files (not for git tracking per user's CLAUDE.md)
STATUS.md
PROGRESS.md
TODO.md

# Specification tracking directory (moved to feature-specific location)
# Keep main project constitution but ignore feature-specific .specify directories
specs/**/.specify/
tools/nodejs/node_modules/

# Generated artifacts and editor configs (060 cleanup)
.opencode/
.mcp.json
.coveragerc
CODEX.md
TABNINE.md

# Stray top-level modules (not part of package)
/common/
/iris_rag/

# Root conftest (tests have their own)
/conftest.py

# Evaluation/report outputs
outputs/reports/
outputs/

# Feature spec dirs for non-active features
specs/025-fixes-for-testing/
specs/043-complete-mcp-tools/
specs/061-implement-fuzzy-matching/