feat(01-01): create Python package scaffold with config system

- pyproject.toml: installable package with bioinformatics dependencies
- Pydantic config schema with validation (ensembl_release >= 100, directory creation)
- YAML config loader with override support
- Default config with Ensembl 113, gnomAD v4.1
- 5 passing tests for config validation and hashing

pyproject.toml

@@ -0,0 +1,55 @@
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "usher-pipeline"
+version = "0.1.0"
+description = "Reproducible pipeline for discovering under-studied cilia/Usher candidate genes"
+requires-python = ">=3.11"
+authors = [
+    {name = "Research Team"}
+]
+readme = "README.md"
+license = {text = "MIT"}
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+dependencies = [
+    "mygene>=3.2.0",
+    "requests>=2.31.0",
+    "requests-cache>=1.1.0",
+    "tenacity>=8.2.0",
+    "pydantic>=2.0",
+    "pydantic-yaml>=1.2.0",
+    "duckdb>=0.9.0",
+    "click>=8.1.0",
+    "polars>=0.19.0",
+    "pyarrow>=14.0.0",
+    "pyyaml>=6.0",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=7.4.0",
+    "pytest-cov>=4.1.0",
+]
+
+[project.scripts]
+usher-pipeline = "usher_pipeline.cli:main"
+
+[tool.setuptools]
+packages = ["usher_pipeline"]
+package-dir = {"" = "src"}
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = ["test_*.py"]
+python_functions = ["test_*"]
+addopts = "-v --strict-markers"