Move all commands to their own .cpp file within the commands directory

All commands are to be moved into their own respective .cpp file.  Example being:

cmd_alias.cpp, contains only an include for a header, and the actual command cmd_alias.

What this does is help us work towards debugging the overall system, it will make the system easier to debug in the long run, while making the overall executable larger, the tradeoff is worth it for debugging purposes.
