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.

pyproject.toml

@@ -1,6 +1,3 @@
-[tool.setuptools]
-py-modules = []
-packages = []
 [project]
 name = "patient-pathway-analysis"
 version = "0.1.0"
@@ -8,25 +5,15 @@ description = "Add your description here"
 readme = "README.md"
 requires-python = ">=3.10"
 dependencies = [
-    "darkdetect==0.8.0",
-    "decorator==5.1.1",
-    "et-xmlfile==1.1.0",
-    "executing==1.2.0",
     "fastparquet>=2024.11.0",
-    "idna==3.4",
-    "itsdangerous==2.1.2",
-    "jedi==0.18.2",
-    "jinja2==3.1.2",
-    "jupyter-core==5.3.1",
-    "numpy==1.25.0",
-    "packaging==23.1",
-    "pandas==2.0.3",
-    "pillow==10.0.0",
-    "plotly==5.15.0",
+    "numpy>=1.25.0",
+    "pandas>=2.0.3",
+    "pillow>=10.0.0",
+    "plotly>=5.15.0",
     "pyarrow>=20.0.0",
-    "python-dateutil==2.8.2",
     "reflex>=0.6.0",
-    "tenacity==8.2.2",
+    "snowflake-connector-python>=3.0.0",
+    "tomli>=2.0.0",
 ]
 
 [project.optional-dependencies]
@@ -36,6 +23,7 @@ test = [
 ]
 
 [tool.pytest.ini_options]
+pythonpath = ["src"]
 testpaths = ["tests"]
 python_files = ["test_*.py"]
 python_classes = ["Test*"]
@@ -52,7 +40,7 @@ markers = [
 ]
 
 [tool.coverage.run]
-source = ["core", "data_processing", "analysis", "visualization", "tools"]
+source = ["src/core", "src/data_processing", "src/analysis", "src/visualization"]
 branch = true
 omit = [
     "*/tests/*",