Fix unreliability of shell tool

[ErikBjare]

Sometimes when using the shell tool it will give output for the last command instead of the current command, making for very confusing output to the LLM.

I'm not sure what causes this, maybe a bad split of the output, maybe triggered by interrupting commands? (which has been somewhat unreliable too)

[0xbrayo]

I have only experienced this with commands that need interactivity like inputting the password for sudo. I guess the second command cannot run until the first command exits, hence the output.