Remove Scallop configuration code redundency

Many of the options in the Scallop configuration in Main.scala is duplicate. For example, all subcommands except for "test" accept the "-s" option. The configuration for the -s is currently duplicated among all the commands. To clean up this code, we should create traits that contain shared options and mix them into the subcommands. See the scallop wiki for how to create traits and mix them in to work with Scallop:

https://github.com/scallop/scallop/wiki/Subcommands#sharing-arguments-with-inheritance