Fix: multiple top-level packages error in Python project (#6370)

### What problem does this PR solve?

This PR resolves the issue of multiple top-level packages being detected
in the Python project, which caused errors when using uv pip install.
The problem occurred because the project had multiple directories files
at the root level, leading to a flat-layout error.
To fix this, the pyproject.toml file was updated to explicitly list the
packages using the [tool.setuptools] section. This ensures that the
correct packages are included during installation, avoiding the
flat-layout error.
Type of change

### Type of change

- [x] Bug Fix (non-breaking change which fixes an issue)

pyproject.toml

@@ -136,6 +136,9 @@ full = [
     "transformers>=4.35.0,<5.0.0"
 ]
 
+[tool.setuptools]
+packages = ['rag', 'api', 'sdk', 'helm','agent', 'deepdoc', 'graphrag', 'flask_session', 'intergrations', 'agentic_reasoning']
+
 [[tool.uv.index]]
 url = "https://mirrors.aliyun.com/pypi/simple"