[Docs]: Regenerate Documentation Following Package Refactor #282

Documentation Update

The project structure has been completely refactored, requiring regeneration and realignment of the Sphinx documentation to reflect the new module layout and import paths. Existing API documentation and autosummary references are now outdated and must be rebuilt to match the current package architecture.

Why Is This Needed?

The previous documentation referenced modules and classes that no longer exist under their original paths. This caused Sphinx build failures due to broken imports (e.g. legacy references such as CodeEntropy.entropy.ConformationalEntropy).

Updating the documentation ensures:

• The API reference reflects the current codebase
• Sphinx builds successfully
• Users are not directed to deprecated or invalid modules
• Future maintenance is simplified following the new structure

Suggested Changes

• Remove previously generated autosummary files and outdated API .rst files
• Regenerate API documentation using sphinx-apidoc based on the new package layout
• Update index.rst to reference the new API structure
• Ensure conf.py correctly includes the project root in sys.path
• Remove or update legacy autosummary references tied to the old module hierarchy
• Rebuild HTML documentation to align with the refactored package

Additional Context

This update follows a full internal restructuring of the CodeEntropy package.
All legacy module paths referenced in previous documentation builds are now invalid and must be replaced by newly generated API documentation.