Adds ls -r option for showing only running programs. I'm sure this can be optimized a bit though
$ pilot ls now has the following behavior:

No options: returns a list of all programs, prefixed with an asterisk if running

Options:
-r List of only running programs
-s List of only stopped programs
-a List of all programs
Updates $ pilot shutdown to use ls -r and only try to shutdown running programs
Merge pull request #8 from patbenatar/running_list

Running list