The CommandToolbox extension allows you to paste in multi-lined commands and click "Overwrite setting" to save the command as such. However, the line breaks are removed whenever someone makes an edit to the extension itself through the extension's options>Edit settings. It seems that edit settings page does not support line returns for the command values or strips them out. Maybe the edit settings page could just clone the UI you use in the CommandToolbox popup it generates when it's called from the dashboard. Just add the ability to change the command name and command.
Customer support service by UserEcho