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.

setup_dev.py

@@ -0,0 +1,13 @@
+"""One-time dev setup: adds src/ to the venv's Python path via a .pth file."""
+
+import site
+import sys
+from pathlib import Path
+
+src_dir = Path(__file__).resolve().parent / "src"
+site_packages = Path(site.getsitepackages()[-1])
+pth_file = site_packages / "patient_pathways.pth"
+
+pth_file.write_text(str(src_dir) + "\n")
+print(f"Created {pth_file}")
+print(f"  -> {src_dir}")