Not only does closing the inline terminal make it annoying if you're using it but it also closes the output box so you don't get to see the result of the command. I can't find where in the run-command code where it causes the panel to close but if the author knows of a way to keep it open or at least re-open the terminal that would be perfect.
Many people use the terminal a lot so having to re-open it after every command makes you wish you'd stuck with just using the terminal command instead of the built-in command in the first place.
