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.

visualization/__init__.py

@@ -1,18 +0,0 @@
-"""
-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",
-]