refactor: Move package files from src/rai/rai/* to src/rai/*

[coderabbitai]

The current package directory structure has modules nested one level deeper than expected by the Poetry configuration in pyproject.toml.

Current structure:

src/rai/rai/*

Expected structure:

src/rai/*

This needs to be refactored to match the package configuration, but some tests are currently failing. This should be addressed after fixing the test issues.

References:

• PR discussion: refactor: rai the package #386 (comment)