refactor: reorganize repository to src/ layout

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.

tests/test_real_data_undefined_rate.py

@@ -8,14 +8,9 @@ directory vs. successfully assigned directories.
 
 import json
 import pandas as pd
-import sys
 from pathlib import Path
 
-# Add project root to path
-project_root = Path(__file__).parent.parent
-sys.path.insert(0, str(project_root))
-
-from tools.data import patient_id, drug_names, department_identification
+from data_processing.transforms import patient_id, drug_names, department_identification
 from core import default_paths