# Python
__pycache__/
*.py[cod]
*$py.class
*.so
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/

# Allow the frontend React apps to commit their own `src/lib` helpers
!apps/ui/webapp/frontend/src/lib/
!apps/ui/webapp/frontend/src/lib/**
!apps/ui/widgets/frontend/src/lib/
!apps/ui/widgets/frontend/src/lib/**
lib64/
parts/
sdist/
var/
wheels/
*.egg-info/
.installed.cfg
*.egg
.ruff_cache/
.pnpm-store/*

# Virtual environments
.venv/
venv/
ENV/
env/

# IDEs
.vscode/
.idea/
.claude/
.cursor/
*.swp
*.swo
*~
.DS_Store

# Testing
.pytest_cache/
.coverage
coverage.xml
htmlcov/
.tox/

# Environment files (actual values - never commit)
.env
.env.local
.env.new_keys
.env.secrets

# Keep config shell files (committed - no secrets)
!config/env-*.sh

# Logs
*.log
debug.log

# Node.js
node_modules/
.pnpm-store/
npm-debug.log*
yarn-debug.log*
yarn-error.log*
package-lock.json

# Build artifacts
*.whl

# OS
.DS_Store
Thumbs.db

# uv
.uv/

# Jupyter
.ipynb_checkpoints/
*.ipynb

# ============================================================================
# Local Development Only - Not Pushed to Remote
# ============================================================================

# Legacy code (for local migration reference only)
legacy/

# Old UI implementations (removed from repo)
Chat-UI/
jupyter-mcp-server/
jupyter-ui/
molstar/
use_these_ui_components/

# Test and debug files (root level only, not in tools/)
/test_*.py
/debug_*.py
/playground.py

# Example conversation files
*_conversation.json
example_conversation.json
demo_conversation.json
protein_solubility_conversation.json

# Molecular structure files
*.pdb
*.cif

# ============================================================================
# Internal Documentation (Not for Public Repo)
# ============================================================================

# Architecture and planning docs (internal)
BACKEND_ARCHITECTURE.md
COMMAND_K_USAGE.md
DISPATCHER_ARCHITECTURE.md
DISPATCHER_EXPLAINED.md
FIX_DEV_CONTAINER_LAG.md
INTERFACES_IMPLEMENTATION_SUMMARY.md
JUPYTER_UI_INTEGRATION_PLAN.md
MONOREPO_STRUCTURE.md
PATH_FIXES.md
PLUGIN_ARCHITECTURE_SUMMARY.md
PROTEIN_IMPORT_WORKFLOW.md
QUERY_DISPATCHER_STATS.md
TOOL_ORCHESTRATION.md
TRACING_ARCHITECTURE.md
USE_SHARED_DISPATCHER.md

# Quickstart/setup docs (internal)
GXL_QUICKSTART.md
INSTALLATION.md
QUICK_REFERENCE.md
QUICK_START.md
SETUP_FOR_NEW_USERS.md
UV_DEV_CONTAINER_GUIDE.md
WHICH_SCRIPT_TO_USE.md

# Status/completion docs (internal)
NOTEPAD_COMPLETE.md
NOTEPAD_READY.md
PUSH_CHECKLIST.md
READY_TO_PUSH.md
SCRATCHPAD_COMPLETE_GUIDE.md
SCRATCHPAD_JUPYTER_DESIGN.md
SCRATCHPAD_NEXT_STEPS.md
SCRATCHPAD_READY.md
SCRATCHPAD_V2_COMPLETE.md

# Runtime/operational docs (internal)
RUN_NOTEBOOK_WITH_FASTMCP.md
RUN_NOTEPAD_SYSTEM.md

# Fix/utility scripts
FIX_IMPORT_ERROR.sh
fix_mcp_api_key.sh
fix_relative_urls.py

# Startup scripts (superseded by gxl command)
start_*.sh

# ============================================================================
# Keep These (Will Be Pushed)
# ============================================================================

# Core documentation (keep)
!README.md
!docs/
!apps/*/README.md
!ui/*/README.md
!packages/*/README.md
!agents/README.md
!REORGANIZATION_COMPLETE.md

# Dev container (keep)
!.devcontainer/

# Dev scripts (keep)
!bin/

# Exclude GUI experimental work (not ready for commit)
apps/ui/gui-exp/

# Exclude CLI session data
# database/

# macOS metadata
.DS_Store
**/.DS_Store

# Playground/testing files
Playground.ipynb
apps/tools/src/mcps/research/data/
apps/tools/src/mcps/fda_mab/data/

database/
sessions/

.pnpm-store/
/fda/
apps/ui/widgets/frontend/.vite/

# FDA MAB PDF data files (too large for git)
fda_mab_pdfs/
apps/tools/src/modules/fda/db/dbs
apps/tools/src/modules/fda/db/jsons/device
apps/tools/src/modules/fda/db/jsons/drug
apps/tools/src/mcps/fda_mab/data/
apps/tools/src/mcps/ctgov/data/
apps/tools/src/modules/fda/docs/
# Google Cloud SDK and tools (local install)
google-cloud-sdk/
google-cloud-cli-*.tar.gz
cloud-sql-proxy

# Data dumps (should not be in repo)
aact-unzipped/
all_fda_mab/

# FDA deprecated docs and data
apps/tools/src/modules/fda/docs_deprecated/
apps/tools/src/mcps/fda/data/

# Scripts (local)
apps/agentgrad/src/agentgrad/experiments/
apps/evals/results/
scripts/db/nct_to_doc_id.csv

# Temporary metadata files
temp_metadata/

# Agent logs
agent_log.md
apps/agentgrad/src/agentgrad/experiments/
apps/evals/results/
scripts/db/*.csv
scripts/db/youtube/*
apps/agentschool/runs/*

# Coverage QA output
packages/coverage-qa/output/

# Tool coverage test pipelines
tests/tool_coverage/

# Custom agent instructions for workflows
docs/agent_instructions/

# FDA CBER data files
scripts/fda/cber/*.json
scripts/fda/cber/approvals_2024.json

**/transcript*.txt
apps/evals/expert_feedback/*
expert_learning_agent_research/
underwriting_guidelines/**
apps/evals/agent_trajectory/*
scripts/db/
.prime/
/configs/
apps/evals/eval_results/
environments/
CLAUDE.md
agents.md
apps/evals/inputs/biorxiv_bench.csv
prime/
gxl-dev-*.json