refactor: restructure modules and update configuration

[dkargatzis]

Refactor: Module Restructure and Configuration Updates

This PR refactors the codebase structure for better organization and maintainability.

Key Changes

Module Reorganization

• Split monolithic config.py into modular package structure
• Consolidated providers and integrations under unified integrations/ structure
• Extracted shared utilities into core/utils/ package
• Moved rule utilities (codeowners, contributors) to rules/utils/

Agent Architecture

• Removed supervisor agent in favor of factory pattern
• Implemented get_agent() factory function for consistent agent instantiation
• Updated all event processors to use factory pattern

Code Improvements

• Fixed OpenAI structured output schema compatibility (removed json_schema_extra, added method="function_calling")
• Updated logging to use rule descriptions instead of deprecated id/name fields
• Removed unused imports and outdated references

Documentation

• Updated all guides to match current .env.example format
• Removed id/name fields from rule examples
• Added watchflow.dev references for better onboarding
• Fixed environment variable names throughout docs

Tests

• Removed supervisor agent tests
• Fixed timeout error type assertion
• All 44 tests passing

Impact

• Improved code organization and maintainability
• Better separation of concerns
• Consistent agent instantiation pattern
• Updated documentation aligned with current structure