Update folder structure and hatch builds to fix issue #2

[rahlk]

Motivation and Context

Packages installed using uv pip install . work correctly within the uv-managed environment, but their CLI entry points may break when executed via system-wide Python (e.g., pyenv), resulting in ModuleNotFoundError.

This PR improves the developer experience by:

• Logging a warning if the CLI script is executed from outside the uv environment
• Adding documentation to clarify how CLI dispatch works with uv and Python environment managers

How Has This Been Tested?

Tested locally with:

• Flat layout Python project (codeanalyzer/)
• pyenv 3.12.11 with global Python
• uv-installed editable package
  Verified that CLI fails outside uv but succeeds with uv run codeanalyzer.

Breaking Changes

None

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• Documentation update

Checklist

• I have read the Codellm-Devkit Documentation
• My code follows the repository's style guidelines
• New and existing tests pass locally
• I have added appropriate error handling
• I have added or updated documentation as needed

Additional context

This PR addresses developer confusion when installing packages via uv while using global Python tools like pyenv. It doesn't change installation behavior but improves clarity and avoids false bug reports.