My custom fish prompt code explained at http://geraldkaszuba.com/tweaking-fish-shell/

fish-time-taken.sh

# Track the last non-empty command. It's a bit of a hack to make sure
# execution time and last command is tracked correctly.
set -l cmd_line (commandline)
if test -n "$cmd_line"
    set -g last_cmd_line $cmd_line
    set -ge new_prompt
else
    set -g new_prompt true
end

# Show last execution time and growl notify if it took long enough
set -l now (date +%s)
if test $last_exec_timestamp
    set -l taken (math $now - $last_exec_timestamp)
    if test $taken -gt 10 -a -n "$new_prompt"
        error taken $taken
        echo "Returned $last_status, took $taken seconds" | \
            growlnotify -s $last_cmd_line
        # Clear the last_cmd_line so pressing enter doesn't repeat
        set -ge last_cmd_line
    end
end
set -g last_exec_timestamp $now

Where should I put this file?