Refactor tool preflight protocol

[sonald]

Summary

• Problem: The execution logic for tools and the LLM session workflow are currently coupled together, which violates design specifications and hinders scalability. All of these components should be fully abstracted from the LLM session.
• Changes:
• Related Issue: #

Change Type

• Bug fix
• Feature
• Refactor
• Docs
• Other

Scope

• Core shell / PTY
• AI agent / LLM
• Skills / Tools
• Security
• Configuration
• CLI / Interface
• Packaging / Installation
• CI/CD
• Documentation

User-visible Changes

Compatibility

• Backward compatible? (Yes/No)
• Config changes? (Yes/No - if yes, describe migration)

Testing

Checklist

• Code follows project style
• Tests added if needed
• Documentation updated if needed

[github-actions]

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[github-actions]

This pull request description looks incomplete. Please update the missing sections below before review.

Missing items:

• User-visible Changes
• Testing