Refactor: Reorganize code for optimized gemini-cli and kilo workflow

[nelsonlin]

Summary

Reorganize the codebase to better optimize the workflow between gemini-cli and kilo code components. This involves grouping files by folder structure, modular or layered architecture, or mapping explicitly to the pipeline steps

Motivation

• Improve code readability and maintainability.
• Clarify module responsibilities, supporting easier onboarding and collaboration.
• Prepare the project for scaling or additional pipeline integrations.
• Save $$$ for token and time - shorten file and code scanning time

Example Approaches

• Organize by pipeline step (e.g., input, process, output folders or packages)
• Abstract common logic into shared modules/layers
• Use consistent naming schemes for gemini-cli and kilo-related files and folders

Acceptance Criteria

• Code is reorganized with a clear rationale (documented in README or architecture notes)
• No breaking changes to core functionality
• Structure supports future development and is easier to navigate
• Token usage and developement time reduce