Fix alias command do not work with command_prefix. 

To fix Pry::Command#run to call command_set.process_line with command_prefix arg, in case \_pry_.config.command_prefix is set.

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 ....

This will fix #1055 .