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.

src/visualization/__init__.py

@@ -0,0 +1,18 @@
+"""
+Visualization package for patient pathway charts.
+
+This package contains functions for generating interactive Plotly visualizations:
+- plotly_generator: Create icicle charts for patient pathway analysis
+"""
+
+from visualization.plotly_generator import (
+    create_icicle_figure,
+    save_figure_html,
+    open_figure_in_browser,
+)
+
+__all__ = [
+    "create_icicle_figure",
+    "save_figure_html",
+    "open_figure_in_browser",
+]