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.

cli/__init__.py

@@ -1,6 +0,0 @@
-"""
-CLI commands for NHS High-Cost Drug Patient Pathway Analysis Tool.
-
-Available commands:
-    python -m cli.refresh_pathways  - Refresh pathway data from Snowflake
-"""