fix(cli): ensure ToolRegistry is initialized in headless mode

[ZxdNoob]

• Add proper error handling in buildSystemMessage() when ToolRegistry is not initialized
• Return empty tools list instead of throwing error to prevent crashes
• Add debug logging for tool registration in config.ts to help diagnose issues
• Log when tools are disabled by configuration for better debugging

Fixes #1099

This fixes the issue where run_shell_command tool was not found in registry
when running in headless mode (e.g., 'echo test | qwen'). The fix ensures
that:

1. ToolRegistry initialization is properly handled in headless mode
2. Tools are properly registered even when configuration filters are applied
3. Better error messages and debugging information are available