Extract load_data() and load_pathway_data() logic from Reflex AppState into standalone functions in src/data_processing/pathway_queries.py. Create thin dash_app/data/queries.py wrapper with DB_PATH resolution.
Move 6 packages (core, config, data_processing, analysis, visualization, cli) into src/ to reduce root clutter. Merge tools/data.py into data_processing/transforms.py. Move docs to docs/. Path resolution via .pth file (setup_dev.py), pytest pythonpath config, and sys.path bootstrap in rxconfig.py and CLI entry points. Clean up pyproject.toml deps (remove stale pins, add snowflake-connector-python). Fix tomllib import for Python 3.10 compatibility. All 113 tests pass.
Andrew Charlwood