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_data_transformations.py

@@ -15,7 +15,7 @@ import pandas as pd
 import pytest
 
 from core.config import PathConfig
-from tools.data import patient_id, drug_names, department_identification
+from data_processing.transforms import patient_id, drug_names, department_identification
 
 
 # ============================================================================