Refactor toolAgent structure

[bhouston]

Description

This PR refactors the toolAgent structure to complete the migration from the deprecated toolAgent.ts file to a modular directory structure.

Changes

• Moved the main toolAgent implementation from index.ts to toolAgentCore.ts
• Updated index.ts to re-export from toolAgentCore.ts and other modules
• Removed the deprecated toolAgent.ts file
• Updated all direct imports to use the new structure
• Updated documentation in README.md

Benefits

• Clearer code organization with more meaningful file names
• Reduced technical debt by removing deprecated file
• All imports now use the recommended path
• Improved maintainability with modular design

Testing

All existing functionality should continue to work with the new structure. No behavioral changes were made, only structural refactoring.

[github-actions]

🎉 This issue has been resolved in version mycoder-agent-v1.0.0 🎉

The release is available on:

• npm package (@latest dist-tag)
• GitHub release

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