Fix alias command do not work with command_prefix. To fix Pry::Command#r...

...un is call command_set.process_line with command_prefix arg, in case Pry.config.command_prefix is set.

#1055
I think this is temporary fix.  I feel command class should not have responsibility to check command_prefix. Because command_prefix is user side matter, so remove prefix from args more near CLI (surface).
So someday refactor it ....