Ports Clean Command to Core

It's all in the title, bro. Ports the clean command to Core and updates the Makefile to get everything to compile as we would like. Addresses #49.
I am going to mess with the actual <code>main.ml</code> file after we port the individual command. Essentially the main file will just export one value
```ocaml
val cs3110-staff : Core.Std.Command.t
```
Which is just a <code>Command.group</code> of all of the individual commands, but I am going to save this for its own issue/PR after the individuals are done because this will require a heavy refactor of the code and I want to keep the tools functional during this whole process.