Refactor the codebase for better organization and improved documentation

The current codebase could benefit from a refactor to improve its structure and maintainability. This issue includes organizing the project files better and improving the inline documentation to make the codebase more understandable and developer-friendly.

**Tasks:**
- Reorganize the folder structure for better separation of concerns (e.g., separate models, controllers, routes).
- Review and improve inline documentation for key functions and classes.
- Update the README and relevant docs to reflect any changes.
- Ensure that tests are still functional after the refactor.

**Expected Outcome:**
A cleaner, more organized codebase with improved documentation to help contributors better understand and navigate the project.