Delete deprecated codes

[sepideh-abedini]

Summary

Clean up the codebase by deleting deprecated code and refactoring the directory and module structure.

Clickup Ticket(s): https://app.clickup.com/t/868gq7yad

Type of Change

• 🐛 Bug fix (non-breaking change that fixes an issue)
• ✨ New feature (non-breaking change that adds functionality)
• 💥 Breaking change (fix or feature that would cause existing functionality to not work as expected)
• 📝 Documentation update
• [ x] 🔧 Refactoring (no functional changes)
• ⚡ Performance improvement
• 🧪 Test improvements
• 🔒 Security fix

Changes Made

• Delete all deprecated source codes that are not used in the current pipe
• pipeline directory now contains one file for each pipeline step
• Related pipeline steps are moved into a shared directory
• Added a prompt directory to the module of each prompt-based step that includes all versions of the prompts used in the step

Testing

• [ x] Tests pass locally (uv run pytest tests/)
• [ x] Type checking passes (uv run mypy <src_dir>)
• [ x] Linting passes (uv run ruff check src_dir/)
• Manual testing performed (describe below)

Checklist

• [ x] Code follows the project's style guidelines
• [ x] Self-review of code completed
• [ x] Documentation updated (if applicable)
• [ x] No sensitive information (API keys, credentials) exposed