Update documentation to reflect new mycoder.config.js configuration system

[bhouston]

Changes

• Remove references to old 'config' CLI commands (config set, config get, config list)
• Update configuration documentation to use mycoder.config.js file
• Update examples throughout the documentation to use the new configuration method
• Update platform-specific setup guides to reflect the new configuration system
• Replace references to the old subAgent tool with the new agentStart and agentMessage tools
• Update the Available Tools section to reflect the new asynchronous agent workflow

This PR addresses the changes made to the MyCoder CLI, which now uses a mycoder.config.js file for configuration instead of the previous CLI-based config commands, and updates the documentation to reflect the new asynchronous agent tools.

Closes #51