How do you prevent CodeRunner from prefixing its console output with [00m[00m[00m[00m[00m?
The culprit probably is line 88 in your prompt.sh:

trap 'echo -ne "\033[00m"' DEBUG


This will output an ANSI escape code to reset the colors and style before the output of every command.

From examining your bash script, this line seems to be unnecessary, because you are resetting the formatting at the end of your prompt here on line 76:

PS1="$status_style"'$fill \t\n'"$BY\$(__name_and_server)$Y\w$G\$(__git_prompt)$RESET$ "


I suggest you just remove line 88 and try it like that.

Somewhat unrelated to this problem, but I also suggest editing line 73 to the following:

local RESET="\[\033[0m\]"


This way you are truly resetting the ANSI styling, whereas before you were setting it to white.