Fix uv run scripts: restore all missing script definitions and enable packaging

- Added all missing script definitions to pyproject.toml [project.scripts]
- Enabled packaging with [tool.uv] package = true
- Added package discovery for scripts* and app* packages
- Created scripts/__init__.py to make scripts a proper Python package
- All uv run commands now work: start, build, build-indexes, etc.

Resolves issue where 'uv run start' failed with 'No such file or directory'

pyproject.toml

@@ -46,4 +46,35 @@ dependencies = [
     "yake>=0.6.0",
 ]
 
+[project.scripts]
+# Application scripts
+start = "scripts.start:main"
+
+# Build scripts  
+build = "scripts.build:main"
+build-all = "scripts.build_all_comprehensive:main"
+build-indexes = "scripts.build_indexes:main"
+build-graphs = "scripts.build_knowledge_graphs:main"
+build-sparse = "scripts.build_sparse_indexes:main"
+
+# Model and data management
+download-models = "scripts.download_models:main"
+setup-datasets = "scripts.setup_datasets:main"
+
+# Upload scripts
+upload-framework = "scripts.upload_dd_framework:main"
+upload-indexes = "scripts.upload_dd_indexes:main"
+upload-vdrs = "scripts.upload_dd_vdrs:main"
+
+# Testing scripts
+run-e2e-tests = "scripts.run_e2e_tests:main"
+verify-test-coverage = "scripts.verify_test_coverage:main"
+test-legal-coreference = "scripts.test_legal_coreference:main"
+
+[tool.setuptools.packages.find]
+include = ["app*", "scripts*"]
+
+[tool.uv]
+package = true
+
 # No build system needed for Spaces - dependencies only

scripts/__init__.py

@@ -0,0 +1 @@
+# Scripts package